Warning: Permanently added '3.87.78.251' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6972644-fedora-39-aarch64 --chroot fedora-39-aarch64 Version: 0.70 PID: 6372 Logging PID: 6373 Task: {'appstream': False, 'background': True, 'build_id': 6972644, 'buildroot_pkgs': [], 'chroot': 'fedora-39-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '6a1e15509098c91f653b329eac361b712a55cecb', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'seqan2', 'package_version': '2.4.0-22', 'project_dirname': 'openblas-0.3.23:pr:2', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-aarch64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/jjames', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/jjames', 'tags': [], 'task_id': '6972644-fedora-39-aarch64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2 /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23:pr:2/seqan2', '/var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2'... Running: git checkout 6a1e15509098c91f653b329eac361b712a55cecb -- cmd: ['git', 'checkout', '6a1e15509098c91f653b329eac361b712a55cecb', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2 rc: 0 stdout: stderr: Note: switching to '6a1e15509098c91f653b329eac361b712a55cecb'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 6a1e155 automatic import of seqan2 Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2 rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading seqan-seqan-v2.4.0.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o seqan-seqan-v2.4.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23:pr:2/seqan2/seqan-seqan-v2.4.0.tar.gz/md5/d899821e295fed0a22e08099f40cbc17/seqan-seqan-v2.4.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 104M 100 104M 0 0 66.0M 0 0:00:01 0:00:01 --:--:-- 66.0M INFO: Reading stdout from command: md5sum seqan-seqan-v2.4.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2/seqan2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706586999.654064 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2/seqan2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706586999.654064 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2/seqan2.spec) Config(fedora-39-aarch64) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-aarch64-bootstrap-1706586999.654064/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-aarch64-bootstrap-1706586999.654064/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/5663d2b0f39cbf19384039014059b724d3e69c4c6585956f862c61164e77495f/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/5663d2b0f39cbf19384039014059b724d3e69c4c6585956f862c61164e77495f/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 173 MB/s | 27 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 183 MB/s | 73 MB 00:00 fedora 53 MB/s | 86 MB 00:01 updates 52 MB/s | 28 MB 00:00 Last metadata expiration check: 0:00:05 ago on Tue Jan 30 03:57:26 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================== Package Arch Version Repository Size ========================================================================================================================== Installing: python3-dnf-plugins-core noarch 4.4.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 496 k dnf-data noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549 k yum noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs aarch64 1:1.14.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 156 k python3-dateutil noarch 1:2.8.2-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus aarch64 1.3.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 146 k python3-distro noarch 1.9.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd aarch64 235-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k Transaction Summary ========================================================================================================================== Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): python3-dateutil-2.8.2-13.fc40.noarch.r 10 MB/s | 345 kB 00:00 (2/11): dbus-libs-1.14.10-3.fc40.aarch64.rpm 4.1 MB/s | 156 kB 00:00 (3/11): python3-distro-1.9.0-3.fc40.noarch.rpm 7.1 MB/s | 45 kB 00:00 (4/11): python3-six-1.16.0-14.fc40.noarch.rpm 12 MB/s | 41 kB 00:00 (5/11): python3-dbus-1.3.2-6.fc40.aarch64.rpm 2.9 MB/s | 146 kB 00:00 (6/11): python3-systemd-235-9.fc40.aarch64.rpm 9.5 MB/s | 101 kB 00:00 (7/11): python3-dnf-plugins-core-4.4.4-3.fc40.n 16 MB/s | 302 kB 00:00 (8/11): dnf-data-4.18.2-1.fc40.noarch.rpm 8.6 MB/s | 39 kB 00:00 (9/11): python3-dnf-4.18.2-1.fc40.noarch.rpm 58 MB/s | 549 kB 00:00 (10/11): yum-4.18.2-1.fc40.noarch.rpm 4.9 MB/s | 37 kB 00:00 (11/11): dnf-4.18.2-1.fc40.noarch.rpm 23 MB/s | 496 kB 00:00 -------------------------------------------------------------------------------- Total 30 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.18.2-1.fc40.noarch 1/15 Upgrading : python3-dnf-4.18.2-1.fc40.noarch 2/15 Upgrading : dnf-4.18.2-1.fc40.noarch 3/15 Running scriptlet: dnf-4.18.2-1.fc40.noarch 3/15 Installing : python3-systemd-235-9.fc40.aarch64 4/15 Installing : python3-six-1.16.0-14.fc40.noarch 5/15 Installing : python3-dateutil-1:2.8.2-13.fc40.noarch 6/15 Installing : python3-distro-1.9.0-3.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-3.fc40.aarch64 8/15 Installing : python3-dbus-1.3.2-6.fc40.aarch64 9/15 Installing : python3-dnf-plugins-core-4.4.4-3.fc40.noarch 10/15 Upgrading : yum-4.18.2-1.fc40.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-3.fc40.aarch64 1/15 Verifying : python3-dateutil-1:2.8.2-13.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-6.fc40.aarch64 3/15 Verifying : python3-distro-1.9.0-3.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.4.4-3.fc40.noarch 5/15 Verifying : python3-six-1.16.0-14.fc40.noarch 6/15 Verifying : python3-systemd-235-9.fc40.aarch64 7/15 Verifying : dnf-4.18.2-1.fc40.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-1.fc40.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-1.fc40.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-1.fc40.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-1.fc40.noarch dnf-data-4.18.2-1.fc40.noarch python3-dnf-4.18.2-1.fc40.noarch yum-4.18.2-1.fc40.noarch Installed: dbus-libs-1:1.14.10-3.fc40.aarch64 python3-dateutil-1:2.8.2-13.fc40.noarch python3-dbus-1.3.2-6.fc40.aarch64 python3-distro-1.9.0-3.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch python3-six-1.16.0-14.fc40.noarch python3-systemd-235-9.fc40.aarch64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-aarch64-1706586999.654064/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.aarch64 rpm-sequoia-1.5.0-1.fc39.aarch64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch yum-4.18.2-1.fc40.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 188 MB/s | 27 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 172 MB/s | 73 MB 00:00 fedora 56 MB/s | 86 MB 00:01 updates 59 MB/s | 28 MB 00:00 Last metadata expiration check: 0:00:05 ago on Tue Jan 30 03:58:20 2024. Dependencies resolved. ========================================================================================================================================= Package Arch Version Repository Size ========================================================================================================================================= Installing group/module packages: bash aarch64 5.2.26-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 aarch64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k coreutils aarch64 9.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M cpio aarch64 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 285 k diffutils aarch64 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 395 k fedora-release-common noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k findutils aarch64 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 489 k gawk aarch64 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M glibc-minimal-langpack aarch64 2.38.9000-35.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 96 k grep aarch64 3.11-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 288 k gzip aarch64 1.12-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 159 k info aarch64 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183 k patch aarch64 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 130 k redhat-rpm-config noarch 280-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build aarch64 4.19.1-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k sed aarch64 4.8-15.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 296 k shadow-utils aarch64 2:4.14.0-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M tar aarch64 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 848 k unzip aarch64 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 185 k util-linux aarch64 2.39.3-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M which aarch64 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k xz aarch64 5.4.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 532 k Installing dependencies: alternatives aarch64 1.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k ansible-srpm-macros noarch 1-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs aarch64 4.0-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k authselect aarch64 1.5.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144 k authselect-libs aarch64 1.5.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 234 k basesystem noarch 11-20.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils aarch64 2.41-31.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.8 M binutils-gold aarch64 2.41-31.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 963 k bzip2-libs aarch64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 862 k coreutils-common aarch64 9.4-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib aarch64 2.9.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83 k crypto-policies noarch 20231204-3.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69 k curl aarch64 8.5.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 369 k cyrus-sasl-lib aarch64 2.1.28-19.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 779 k debugedit aarch64 5.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 79 k dwz aarch64 0.15-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 136 k ed aarch64 1.20-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 81 k efi-srpm-macros noarch 5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils aarch64 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 555 k elfutils-debuginfod-client aarch64 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k elfutils-default-yama-scope noarch 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf aarch64 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 194 k elfutils-libs aarch64 0.190-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 260 k fedora-gpg-keys noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 119 k fedora-release noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 10 k fedora-release-identity-basic noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k fedora-repos noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.3 k fedora-repos-rawhide noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.9 k file aarch64 5.45-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 49 k file-libs aarch64 5.45-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 763 k filesystem aarch64 3.18-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M fonts-srpm-macros noarch 1:2.0.5-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 k 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Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-8.fc40.aarch64 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.4.fc40.aarch64 1/152 Running scriptlet: libgcc-14.0.1-0.4.fc40.aarch64 1/152 Installing : crypto-policies-20231204-3.git1e3a2e4.fc40.noarc 2/152 Running scriptlet: crypto-policies-20231204-3.git1e3a2e4.fc40.noarc 2/152 Installing : fedora-release-identity-basic-40-0.29.noarch 3/152 Installing : fedora-repos-rawhide-40-0.2.noarch 4/152 Installing : fedora-gpg-keys-40-0.2.noarch 5/152 Installing : fedora-repos-40-0.2.noarch 6/152 Installing : fedora-release-common-40-0.29.noarch 7/152 Installing : fedora-release-40-0.29.noarch 8/152 Installing : setup-2.14.5-2.fc40.noarch 9/152 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-2.fc40.noarch 9/152 Installing : filesystem-3.18-8.fc40.aarch64 10/152 Installing : basesystem-11-20.fc40.noarch 11/152 Installing : rust-srpm-macros-25.2-3.fc40.noarch 12/152 Installing : 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redhat-rpm-config-280-1.fc40.noarch 147/152 Installing : rpm-build-4.19.1-4.fc40.aarch64 148/152 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.3-4.fc40.aarch64 150/152 Installing : which-2.21-41.fc40.aarch64 151/152 Installing : info-7.1-2.fc40.aarch64 152/152 Running scriptlet: filesystem-3.18-8.fc40.aarch64 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.5.0-3.fc40.aarch64 152/152 Running scriptlet: rpm-4.19.1-4.fc40.aarch64 152/152 Running scriptlet: info-7.1-2.fc40.aarch64 152/152 Installed: alternatives-1.26-3.fc40.aarch64 ansible-srpm-macros-1-14.fc40.noarch audit-libs-4.0-7.fc40.aarch64 authselect-1.5.0-3.fc40.aarch64 authselect-libs-1.5.0-3.fc40.aarch64 basesystem-11-20.fc40.noarch bash-5.2.26-2.fc40.aarch64 binutils-2.41-31.fc40.aarch64 binutils-gold-2.41-31.fc40.aarch64 bzip2-1.0.8-18.fc40.aarch64 bzip2-libs-1.0.8-18.fc40.aarch64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.4-5.fc40.aarch64 coreutils-common-9.4-5.fc40.aarch64 cpio-2.15-1.fc40.aarch64 cracklib-2.9.11-5.fc40.aarch64 crypto-policies-20231204-3.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.aarch64 cyrus-sasl-lib-2.1.28-19.fc40.aarch64 debugedit-5.0-14.fc40.aarch64 diffutils-3.10-5.fc40.aarch64 dwz-0.15-5.fc40.aarch64 ed-1.20-2.fc40.aarch64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.190-6.fc40.aarch64 elfutils-debuginfod-client-0.190-6.fc40.aarch64 elfutils-default-yama-scope-0.190-6.fc40.noarch elfutils-libelf-0.190-6.fc40.aarch64 elfutils-libs-0.190-6.fc40.aarch64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-3.fc40.aarch64 file-libs-5.45-3.fc40.aarch64 filesystem-3.18-8.fc40.aarch64 findutils-1:4.9.0-8.fc40.aarch64 fonts-srpm-macros-1:2.0.5-14.fc40.noarch forge-srpm-macros-0.2.0-3.fc40.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.aarch64 gdb-minimal-14.1-8.fc40.aarch64 gdbm-1:1.23-6.fc40.aarch64 gdbm-libs-1:1.23-6.fc40.aarch64 ghc-srpm-macros-1.6.1-5.fc40.noarch glibc-2.38.9000-35.fc40.aarch64 glibc-common-2.38.9000-35.fc40.aarch64 glibc-gconv-extra-2.38.9000-35.fc40.aarch64 glibc-minimal-langpack-2.38.9000-35.fc40.aarch64 gmp-1:6.2.1-8.fc40.aarch64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.3.1-3.fc40.noarch grep-3.11-7.fc40.aarch64 gzip-1.12-8.fc40.aarch64 info-7.1-2.fc40.aarch64 jansson-2.13.1-9.fc40.aarch64 kernel-srpm-macros-1.0-22.fc40.noarch keyutils-libs-1.6.3-3.fc40.aarch64 krb5-libs-1.21.2-5.fc40.aarch64 libacl-2.3.2-1.fc40.aarch64 libarchive-3.7.2-3.fc40.aarch64 libattr-2.5.2-3.fc40.aarch64 libblkid-2.39.3-4.fc40.aarch64 libbrotli-1.1.0-3.fc40.aarch64 libcap-2.69-3.fc40.aarch64 libcap-ng-0.8.4-4.fc40.aarch64 libcom_err-1.47.0-4.fc40.aarch64 libcurl-8.5.0-2.fc40.aarch64 libeconf-0.5.2-3.fc40.aarch64 libevent-2.1.12-11.fc40.aarch64 libfdisk-2.39.3-4.fc40.aarch64 libffi-3.4.4-7.fc40.aarch64 libgcc-14.0.1-0.4.fc40.aarch64 libgomp-14.0.1-0.4.fc40.aarch64 libidn2-2.3.7-1.fc40.aarch64 libmount-2.39.3-4.fc40.aarch64 libnghttp2-1.59.0-2.fc40.aarch64 libnsl2-2.0.1-1.fc40.aarch64 libpkgconf-1.9.5-4.fc40.aarch64 libpsl-0.21.5-3.fc40.aarch64 libpwquality-1.4.5-9.fc40.aarch64 libselinux-3.6-4.fc40.aarch64 libsemanage-3.6-3.fc40.aarch64 libsepol-3.6-3.fc40.aarch64 libsmartcols-2.39.3-4.fc40.aarch64 libssh-0.10.6-4.fc40.aarch64 libssh-config-0.10.6-4.fc40.noarch libstdc++-14.0.1-0.4.fc40.aarch64 libtasn1-4.19.0-6.fc40.aarch64 libtirpc-1.3.4-1.rc2.fc40.2.aarch64 libunistring-1.1-7.fc40.aarch64 libutempter-1.2.1-13.fc40.aarch64 libuuid-2.39.3-4.fc40.aarch64 libverto-0.3.2-8.fc40.aarch64 libxcrypt-4.4.36-5.fc40.aarch64 libxml2-2.12.4-3.fc40.aarch64 libzstd-1.5.5-5.fc40.aarch64 lua-libs-5.4.6-5.fc40.aarch64 lua-srpm-macros-1-11.fc40.noarch lz4-libs-1.9.4-6.fc40.aarch64 mpfr-4.2.1-3.fc40.aarch64 ncurses-base-6.4-11.20240113.fc40.noarch ncurses-libs-6.4-11.20240113.fc40.aarch64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-16.fc40.noarch openldap-2.6.6-1.fc39.aarch64 openssl-libs-1:3.1.4-4.fc40.aarch64 p11-kit-0.25.3-1.fc40.aarch64 p11-kit-trust-0.25.3-1.fc40.aarch64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.0-1.fc40.aarch64 pam-libs-1.6.0-1.fc40.aarch64 patch-2.7.6-24.fc40.aarch64 pcre2-10.42-2.fc40.2.aarch64 pcre2-syntax-10.42-2.fc40.2.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-1.9.5-4.fc40.aarch64 pkgconf-m4-1.9.5-4.fc40.noarch pkgconf-pkg-config-1.9.5-4.fc40.aarch64 popt-1.19-6.fc40.aarch64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-3.fc40.noarch qt6-srpm-macros-6.6.1-5.fc40.noarch readline-8.2-8.fc40.aarch64 redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-4.fc40.aarch64 rpm-build-4.19.1-4.fc40.aarch64 rpm-build-libs-4.19.1-4.fc40.aarch64 rpm-libs-4.19.1-4.fc40.aarch64 rpm-sequoia-1.6.0-2.fc40.aarch64 rust-srpm-macros-25.2-3.fc40.noarch sed-4.8-15.fc40.aarch64 setup-2.14.5-2.fc40.noarch shadow-utils-2:4.14.0-4.fc40.aarch64 sqlite-libs-3.45.0-2.fc40.aarch64 systemd-libs-255.3-1.fc40.aarch64 tar-2:1.35-3.fc40.aarch64 unzip-6.0-63.fc40.aarch64 util-linux-2.39.3-4.fc40.aarch64 util-linux-core-2.39.3-4.fc40.aarch64 which-2.21-41.fc40.aarch64 xxhash-libs-0.8.2-2.fc40.aarch64 xz-5.4.6-1.fc40.aarch64 xz-libs-5.4.6-1.fc40.aarch64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.aarch64 zlib-ng-compat-2.1.6-2.fc40.aarch64 zstd-1.5.5-5.fc40.aarch64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-3.fc40.aarch64 ansible-srpm-macros-1-14.fc40.noarch audit-libs-4.0-7.fc40.aarch64 authselect-1.5.0-3.fc40.aarch64 authselect-libs-1.5.0-3.fc40.aarch64 basesystem-11-20.fc40.noarch bash-5.2.26-2.fc40.aarch64 binutils-2.41-31.fc40.aarch64 binutils-gold-2.41-31.fc40.aarch64 bzip2-1.0.8-18.fc40.aarch64 bzip2-libs-1.0.8-18.fc40.aarch64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.4-5.fc40.aarch64 coreutils-common-9.4-5.fc40.aarch64 cpio-2.15-1.fc40.aarch64 cracklib-2.9.11-5.fc40.aarch64 crypto-policies-20231204-3.git1e3a2e4.fc40.noarch curl-8.5.0-2.fc40.aarch64 cyrus-sasl-lib-2.1.28-19.fc40.aarch64 debugedit-5.0-14.fc40.aarch64 diffutils-3.10-5.fc40.aarch64 dwz-0.15-5.fc40.aarch64 ed-1.20-2.fc40.aarch64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.190-6.fc40.aarch64 elfutils-debuginfod-client-0.190-6.fc40.aarch64 elfutils-default-yama-scope-0.190-6.fc40.noarch elfutils-libelf-0.190-6.fc40.aarch64 elfutils-libs-0.190-6.fc40.aarch64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-3.fc40.aarch64 file-libs-5.45-3.fc40.aarch64 filesystem-3.18-8.fc40.aarch64 findutils-4.9.0-8.fc40.aarch64 fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.2.0-3.fc40.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.aarch64 gdb-minimal-14.1-8.fc40.aarch64 gdbm-1.23-6.fc40.aarch64 gdbm-libs-1.23-6.fc40.aarch64 ghc-srpm-macros-1.6.1-5.fc40.noarch glibc-2.38.9000-35.fc40.aarch64 glibc-common-2.38.9000-35.fc40.aarch64 glibc-gconv-extra-2.38.9000-35.fc40.aarch64 glibc-minimal-langpack-2.38.9000-35.fc40.aarch64 gmp-6.2.1-8.fc40.aarch64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.3.1-3.fc40.noarch grep-3.11-7.fc40.aarch64 gzip-1.12-8.fc40.aarch64 info-7.1-2.fc40.aarch64 jansson-2.13.1-9.fc40.aarch64 kernel-srpm-macros-1.0-22.fc40.noarch keyutils-libs-1.6.3-3.fc40.aarch64 krb5-libs-1.21.2-5.fc40.aarch64 libacl-2.3.2-1.fc40.aarch64 libarchive-3.7.2-3.fc40.aarch64 libattr-2.5.2-3.fc40.aarch64 libblkid-2.39.3-4.fc40.aarch64 libbrotli-1.1.0-3.fc40.aarch64 libcap-2.69-3.fc40.aarch64 libcap-ng-0.8.4-4.fc40.aarch64 libcom_err-1.47.0-4.fc40.aarch64 libcurl-8.5.0-2.fc40.aarch64 libeconf-0.5.2-3.fc40.aarch64 libevent-2.1.12-11.fc40.aarch64 libfdisk-2.39.3-4.fc40.aarch64 libffi-3.4.4-7.fc40.aarch64 libgcc-14.0.1-0.4.fc40.aarch64 libgomp-14.0.1-0.4.fc40.aarch64 libidn2-2.3.7-1.fc40.aarch64 libmount-2.39.3-4.fc40.aarch64 libnghttp2-1.59.0-2.fc40.aarch64 libnsl2-2.0.1-1.fc40.aarch64 libpkgconf-1.9.5-4.fc40.aarch64 libpsl-0.21.5-3.fc40.aarch64 libpwquality-1.4.5-9.fc40.aarch64 libselinux-3.6-4.fc40.aarch64 libsemanage-3.6-3.fc40.aarch64 libsepol-3.6-3.fc40.aarch64 libsmartcols-2.39.3-4.fc40.aarch64 libssh-0.10.6-4.fc40.aarch64 libssh-config-0.10.6-4.fc40.noarch libstdc++-14.0.1-0.4.fc40.aarch64 libtasn1-4.19.0-6.fc40.aarch64 libtirpc-1.3.4-1.rc2.fc40.2.aarch64 libunistring-1.1-7.fc40.aarch64 libutempter-1.2.1-13.fc40.aarch64 libuuid-2.39.3-4.fc40.aarch64 libverto-0.3.2-8.fc40.aarch64 libxcrypt-4.4.36-5.fc40.aarch64 libxml2-2.12.4-3.fc40.aarch64 libzstd-1.5.5-5.fc40.aarch64 lua-libs-5.4.6-5.fc40.aarch64 lua-srpm-macros-1-11.fc40.noarch lz4-libs-1.9.4-6.fc40.aarch64 mpfr-4.2.1-3.fc40.aarch64 ncurses-base-6.4-11.20240113.fc40.noarch ncurses-libs-6.4-11.20240113.fc40.aarch64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-16.fc40.noarch openldap-2.6.6-1.fc39.aarch64 openssl-libs-3.1.4-4.fc40.aarch64 p11-kit-0.25.3-1.fc40.aarch64 p11-kit-trust-0.25.3-1.fc40.aarch64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.0-1.fc40.aarch64 pam-libs-1.6.0-1.fc40.aarch64 patch-2.7.6-24.fc40.aarch64 pcre2-10.42-2.fc40.2.aarch64 pcre2-syntax-10.42-2.fc40.2.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-1.9.5-4.fc40.aarch64 pkgconf-m4-1.9.5-4.fc40.noarch pkgconf-pkg-config-1.9.5-4.fc40.aarch64 popt-1.19-6.fc40.aarch64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-7.fc40.noarch qt5-srpm-macros-5.15.12-3.fc40.noarch qt6-srpm-macros-6.6.1-5.fc40.noarch readline-8.2-8.fc40.aarch64 redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-4.fc40.aarch64 rpm-build-4.19.1-4.fc40.aarch64 rpm-build-libs-4.19.1-4.fc40.aarch64 rpm-libs-4.19.1-4.fc40.aarch64 rpm-sequoia-1.6.0-2.fc40.aarch64 rust-srpm-macros-25.2-3.fc40.noarch sed-4.8-15.fc40.aarch64 setup-2.14.5-2.fc40.noarch shadow-utils-4.14.0-4.fc40.aarch64 sqlite-libs-3.45.0-2.fc40.aarch64 systemd-libs-255.3-1.fc40.aarch64 tar-1.35-3.fc40.aarch64 unzip-6.0-63.fc40.aarch64 util-linux-2.39.3-4.fc40.aarch64 util-linux-core-2.39.3-4.fc40.aarch64 which-2.21-41.fc40.aarch64 xxhash-libs-0.8.2-2.fc40.aarch64 xz-5.4.6-1.fc40.aarch64 xz-libs-5.4.6-1.fc40.aarch64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.aarch64 zlib-ng-compat-2.1.6-2.fc40.aarch64 zstd-1.5.5-5.fc40.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706486400 Wrote: /builddir/build/SRPMS/seqan2-2.4.0-22.fc40.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-3p3uz1h6/seqan2/seqan2.spec) Config(child) 2 minutes 3 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/seqan2-2.4.0-22.fc40.src.rpm) Config(fedora-39-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-aarch64-bootstrap-1706586999.654064/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-aarch64-bootstrap-1706586999.654064/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-aarch64-1706586999.654064/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.aarch64 rpm-sequoia-1.5.0-1.fc39.aarch64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-3.fc40.noarch yum-4.18.2-1.fc40.noarch Finish: chroot init Start: build phase for seqan2-2.4.0-22.fc40.src.rpm Start: build setup for seqan2-2.4.0-22.fc40.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706486400 Wrote: /builddir/build/SRPMS/seqan2-2.4.0-22.fc40.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 79 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 137 kB/s | 3.8 kB 00:00 fedora 48 kB/s | 14 kB 00:00 updates 433 kB/s | 13 kB 00:00 Dependencies resolved. =================================================================================================================================== Package Arch Version Repository Size =================================================================================================================================== Installing: boost-devel aarch64 1.83.0-2.fc40 copr_base 12 M bzip2-devel aarch64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 214 k cmake aarch64 3.27.7-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.4 M gcc-c++ aarch64 14.0.1-0.4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 M libstdc++-static aarch64 14.0.1-0.4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 879 k llvm-devel aarch64 17.0.6-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 3.6 M make aarch64 1:4.4.1-6.fc40 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0.6.3-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k xorg-x11-proto-devel noarch 2023.2-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 263 k xz-devel aarch64 5.4.6-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 62 k Transaction Summary =================================================================================================================================== Install 199 Packages Total download size: 271 M Installed size: 1.3 G Downloading Packages: (1/199): boost-1.83.0-2.fc40.aarch64.rpm 841 kB/s | 15 kB 00:00 (2/199): boost-atomic-1.83.0-2.fc40.aarch64.rpm 1.1 MB/s | 20 kB 00:00 (3/199): boost-chrono-1.83.0-2.fc40.aarch64.rpm 1.4 MB/s | 26 kB 00:00 (4/199): boost-context-1.83.0-2.fc40.aarch64.rp 11 MB/s | 18 kB 00:00 (5/199): boost-contract-1.83.0-2.fc40.aarch64.r 24 MB/s | 44 kB 00:00 (6/199): boost-container-1.83.0-2.fc40.aarch64. 7.4 MB/s | 40 kB 00:00 (7/199): boost-coroutine-1.83.0-2.fc40.aarch64. 6.9 MB/s | 21 kB 00:00 (8/199): boost-date-time-1.83.0-2.fc40.aarch64. 5.8 MB/s | 16 kB 00:00 (9/199): boost-fiber-1.83.0-2.fc40.aarch64.rpm 12 MB/s | 43 kB 00:00 (10/199): boost-filesystem-1.83.0-2.fc40.aarch6 6.4 MB/s | 65 kB 00:00 (11/199): boost-graph-1.83.0-2.fc40.aarch64.rpm 22 MB/s | 143 kB 00:00 (12/199): boost-iostreams-1.83.0-2.fc40.aarch64 8.1 MB/s | 41 kB 00:00 (13/199): boost-json-1.83.0-2.fc40.aarch64.rpm 35 MB/s | 142 kB 00:00 (14/199): boost-locale-1.83.0-2.fc40.aarch64.rp 35 MB/s | 201 kB 00:00 (15/199): boost-log-1.83.0-2.fc40.aarch64.rpm 66 MB/s | 459 kB 00:00 (16/199): boost-devel-1.83.0-2.fc40.aarch64.rpm 256 MB/s | 12 MB 00:00 (17/199): boost-math-1.83.0-2.fc40.aarch64.rpm 18 MB/s | 260 kB 00:00 (18/199): boost-nowide-1.83.0-2.fc40.aarch64.rp 1.6 MB/s | 21 kB 00:00 (19/199): boost-numpy3-1.83.0-2.fc40.aarch64.rp 16 MB/s | 29 kB 00:00 (20/199): boost-program-options-1.83.0-2.fc40.a 38 MB/s | 104 kB 00:00 (21/199): boost-python3-1.83.0-2.fc40.aarch64.r 31 MB/s | 90 kB 00:00 (22/199): boost-random-1.83.0-2.fc40.aarch64.rp 11 MB/s | 25 kB 00:00 (23/199): boost-regex-1.83.0-2.fc40.aarch64.rpm 53 MB/s | 109 kB 00:00 (24/199): boost-stacktrace-1.83.0-2.fc40.aarch6 20 MB/s | 30 kB 00:00 (25/199): boost-system-1.83.0-2.fc40.aarch64.rp 10 MB/s | 16 kB 00:00 (26/199): boost-test-1.83.0-2.fc40.aarch64.rpm 65 MB/s | 230 kB 00:00 (27/199): boost-thread-1.83.0-2.fc40.aarch64.rp 22 MB/s | 60 kB 00:00 (28/199): boost-serialization-1.83.0-2.fc40.aar 19 MB/s | 132 kB 00:00 (29/199): boost-timer-1.83.0-2.fc40.aarch64.rpm 13 MB/s | 22 kB 00:00 (30/199): boost-wave-1.83.0-2.fc40.aarch64.rpm 76 MB/s | 207 kB 00:00 (31/199): boost-type_erasure-1.83.0-2.fc40.aarc 8.6 MB/s | 33 kB 00:00 (32/199): graphite2-1.3.14-15.fc40.aarch64.rpm 44 MB/s | 93 kB 00:00 (33/199): graphite2-devel-1.3.14-15.fc40.aarch6 12 MB/s | 21 kB 00:00 (34/199): python3-numpy-1.26.2-4.fc40.aarch64.r 266 MB/s | 6.4 MB 00:00 (35/199): abattis-cantarell-vf-fonts-0.301-12.f 2.8 MB/s | 120 kB 00:00 (36/199): alsa-lib-1.2.11-2.fc40.aarch64.rpm 11 MB/s | 497 kB 00:00 (37/199): annobin-docs-12.38-1.fc40.noarch.rpm 4.5 MB/s | 90 kB 00:00 (38/199): brotli-1.1.0-3.fc40.aarch64.rpm 5.8 MB/s | 20 kB 00:00 (39/199): brotli-devel-1.1.0-3.fc40.aarch64.rpm 9.2 MB/s | 34 kB 00:00 (40/199): annobin-plugin-gcc-12.38-1.fc40.aarch 73 MB/s | 956 kB 00:00 (41/199): bzip2-devel-1.0.8-18.fc40.aarch64.rpm 20 MB/s | 214 kB 00:00 (42/199): cairo-1.18.0-3.fc40.aarch64.rpm 61 MB/s | 701 kB 00:00 (43/199): cmake-filesystem-3.27.7-1.fc40.aarch6 1.8 MB/s | 19 kB 00:00 (44/199): cmake-rpm-macros-3.27.7-1.fc40.noarch 2.1 MB/s | 19 kB 00:00 (45/199): cmake-data-3.27.7-1.fc40.noarch.rpm 71 MB/s | 1.7 MB 00:00 (46/199): dbus-libs-1.14.10-3.fc40.aarch64.rpm 25 MB/s | 156 kB 00:00 (47/199): cmake-3.27.7-1.fc40.aarch64.rpm 151 MB/s | 7.4 MB 00:00 (48/199): default-fonts-core-sans-4.0-11.fc40.n 1.5 MB/s | 25 kB 00:00 (49/199): expat-2.5.0-5.fc40.aarch64.rpm 13 MB/s | 108 kB 00:00 (50/199): emacs-filesystem-29.2-3.fc40.noarch.r 608 kB/s | 7.8 kB 00:00 (51/199): flexiblas-netlib-3.4.1-3.fc40.aarch64 180 MB/s | 2.7 MB 00:00 (52/199): flexiblas-3.4.1-3.fc40.aarch64.rpm 1.3 MB/s | 25 kB 00:00 (53/199): flexiblas-openblas-openmp-3.4.1-3.fc4 3.0 MB/s | 17 kB 00:00 (54/199): fontconfig-2.15.0-3.fc40.aarch64.rpm 33 MB/s | 262 kB 00:00 (55/199): fontconfig-devel-2.15.0-3.fc40.aarch6 24 MB/s | 129 kB 00:00 (56/199): cpp-14.0.1-0.4.fc40.aarch64.rpm 134 MB/s | 11 MB 00:00 (57/199): fonts-filesystem-2.0.5-14.fc40.noarch 565 kB/s | 8.2 kB 00:00 (58/199): freetype-2.13.2-1.fc40.aarch64.rpm 27 MB/s | 405 kB 00:00 (59/199): gc-8.2.2-6.fc40.aarch64.rpm 27 MB/s | 110 kB 00:00 (60/199): freetype-devel-2.13.2-1.fc40.aarch64. 100 MB/s | 913 kB 00:00 (61/199): gcc-plugin-annobin-14.0.1-0.4.fc40.aa 5.6 MB/s | 34 kB 00:00 (62/199): gettext-0.22-4.fc40.aarch64.rpm 38 MB/s | 1.0 MB 00:00 (63/199): gettext-envsubst-0.22-4.fc40.aarch64. 3.2 MB/s | 36 kB 00:00 (64/199): 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jbigkit-libs-2.1-29.fc40.aarch64.rpm 7.9 MB/s | 53 kB 00:00 (79/199): jsoncpp-1.9.5-7.fc40.aarch64.rpm 19 MB/s | 91 kB 00:00 (80/199): guile30-3.0.7-12.fc40.aarch64.rpm 181 MB/s | 8.0 MB 00:00 (81/199): lcms2-2.16-3.fc40.aarch64.rpm 14 MB/s | 184 kB 00:00 (82/199): kernel-headers-6.8.0-0.rc1.12.fc40.1. 71 MB/s | 1.4 MB 00:00 (83/199): libICE-1.1.1-3.fc40.aarch64.rpm 20 MB/s | 74 kB 00:00 (84/199): libICE-devel-1.1.1-3.fc40.aarch64.rpm 11 MB/s | 46 kB 00:00 (85/199): libSM-1.2.4-3.fc40.aarch64.rpm 13 MB/s | 43 kB 00:00 (86/199): libSM-devel-1.2.4-3.fc40.aarch64.rpm 3.5 MB/s | 12 kB 00:00 (87/199): libX11-1.8.7-3.fc40.aarch64.rpm 96 MB/s | 647 kB 00:00 (88/199): libX11-common-1.8.7-3.fc40.noarch.rpm 22 MB/s | 144 kB 00:00 (89/199): libX11-xcb-1.8.7-3.fc40.aarch64.rpm 3.4 MB/s | 12 kB 00:00 (90/199): libXau-1.0.11-6.fc40.aarch64.rpm 8.1 MB/s | 32 kB 00:00 (91/199): libX11-devel-1.8.7-3.fc40.aarch64.rpm 78 MB/s | 912 kB 00:00 (92/199): libXau-devel-1.0.11-6.fc40.aarch64.rp 3.5 MB/s | 14 kB 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boost-contract-1.83.0-2.fc40.aarch64 boost-coroutine-1.83.0-2.fc40.aarch64 boost-date-time-1.83.0-2.fc40.aarch64 boost-devel-1.83.0-2.fc40.aarch64 boost-fiber-1.83.0-2.fc40.aarch64 boost-filesystem-1.83.0-2.fc40.aarch64 boost-graph-1.83.0-2.fc40.aarch64 boost-iostreams-1.83.0-2.fc40.aarch64 boost-json-1.83.0-2.fc40.aarch64 boost-locale-1.83.0-2.fc40.aarch64 boost-log-1.83.0-2.fc40.aarch64 boost-math-1.83.0-2.fc40.aarch64 boost-nowide-1.83.0-2.fc40.aarch64 boost-numpy3-1.83.0-2.fc40.aarch64 boost-program-options-1.83.0-2.fc40.aarch64 boost-python3-1.83.0-2.fc40.aarch64 boost-random-1.83.0-2.fc40.aarch64 boost-regex-1.83.0-2.fc40.aarch64 boost-serialization-1.83.0-2.fc40.aarch64 boost-stacktrace-1.83.0-2.fc40.aarch64 boost-system-1.83.0-2.fc40.aarch64 boost-test-1.83.0-2.fc40.aarch64 boost-thread-1.83.0-2.fc40.aarch64 boost-timer-1.83.0-2.fc40.aarch64 boost-type_erasure-1.83.0-2.fc40.aarch64 boost-wave-1.83.0-2.fc40.aarch64 brotli-1.1.0-3.fc40.aarch64 brotli-devel-1.1.0-3.fc40.aarch64 bzip2-devel-1.0.8-18.fc40.aarch64 cairo-1.18.0-3.fc40.aarch64 cmake-3.27.7-1.fc40.aarch64 cmake-data-3.27.7-1.fc40.noarch cmake-filesystem-3.27.7-1.fc40.aarch64 cmake-rpm-macros-3.27.7-1.fc40.noarch cpp-14.0.1-0.4.fc40.aarch64 dbus-libs-1:1.14.10-3.fc40.aarch64 default-fonts-core-sans-4.0-11.fc40.noarch emacs-filesystem-1:29.2-3.fc40.noarch expat-2.5.0-5.fc40.aarch64 flexiblas-3.4.1-3.fc40.aarch64 flexiblas-netlib-3.4.1-3.fc40.aarch64 flexiblas-openblas-openmp-3.4.1-3.fc40.aarch64 fontconfig-2.15.0-3.fc40.aarch64 fontconfig-devel-2.15.0-3.fc40.aarch64 fonts-filesystem-1:2.0.5-14.fc40.noarch freetype-2.13.2-1.fc40.aarch64 freetype-devel-2.13.2-1.fc40.aarch64 gc-8.2.2-6.fc40.aarch64 gcc-14.0.1-0.4.fc40.aarch64 gcc-c++-14.0.1-0.4.fc40.aarch64 gcc-plugin-annobin-14.0.1-0.4.fc40.aarch64 gettext-0.22-4.fc40.aarch64 gettext-envsubst-0.22-4.fc40.aarch64 gettext-libs-0.22-4.fc40.aarch64 gettext-runtime-0.22-4.fc40.aarch64 gl-manpages-1.1-31.20190306.fc40.noarch glib2-2.79.1-1.fc40.aarch64 glib2-devel-2.79.1-1.fc40.aarch64 glibc-devel-2.38.9000-35.fc40.aarch64 gnutls-3.8.3-2.fc40.aarch64 google-noto-fonts-common-20230801-6.fc40.noarch google-noto-sans-vf-fonts-20230801-6.fc40.noarch graphite2-1.3.14-15.fc40.aarch64 graphite2-devel-1.3.14-15.fc40.aarch64 guile30-3.0.7-12.fc40.aarch64 harfbuzz-8.3.0-4.fc40.aarch64 harfbuzz-devel-8.3.0-4.fc40.aarch64 harfbuzz-icu-8.3.0-4.fc40.aarch64 jbigkit-libs-2.1-29.fc40.aarch64 jsoncpp-1.9.5-7.fc40.aarch64 kernel-headers-6.8.0-0.rc1.12.fc40.1.aarch64 lcms2-2.16-3.fc40.aarch64 libICE-1.1.1-3.fc40.aarch64 libICE-devel-1.1.1-3.fc40.aarch64 libSM-1.2.4-3.fc40.aarch64 libSM-devel-1.2.4-3.fc40.aarch64 libX11-1.8.7-3.fc40.aarch64 libX11-common-1.8.7-3.fc40.noarch libX11-devel-1.8.7-3.fc40.aarch64 libX11-xcb-1.8.7-3.fc40.aarch64 libXau-1.0.11-6.fc40.aarch64 libXau-devel-1.0.11-6.fc40.aarch64 libXcursor-1.2.1-7.fc40.aarch64 libXcursor-devel-1.2.1-7.fc40.aarch64 libXext-1.3.5-6.fc40.aarch64 libXext-devel-1.3.5-6.fc40.aarch64 libXfixes-6.0.1-3.fc40.aarch64 libXfixes-devel-6.0.1-3.fc40.aarch64 libXft-2.3.8-6.fc40.aarch64 libXft-devel-2.3.8-6.fc40.aarch64 libXi-1.8.1-5.fc40.aarch64 libXi-devel-1.8.1-5.fc40.aarch64 libXinerama-1.1.5-6.fc40.aarch64 libXinerama-devel-1.1.5-6.fc40.aarch64 libXrandr-1.5.4-3.fc40.aarch64 libXrandr-devel-1.5.4-3.fc40.aarch64 libXrender-0.9.11-6.fc40.aarch64 libXrender-devel-0.9.11-6.fc40.aarch64 libXt-1.3.0-3.fc40.aarch64 libXt-devel-1.3.0-3.fc40.aarch64 libXv-1.0.12-3.fc40.aarch64 libXv-devel-1.0.12-3.fc40.aarch64 libXxf86vm-1.1.5-6.fc40.aarch64 libasan-14.0.1-0.4.fc40.aarch64 libatomic-14.0.1-0.4.fc40.aarch64 libb2-0.98.1-11.fc40.aarch64 libblkid-devel-2.39.3-4.fc40.aarch64 libdrm-2.4.120-3.fc40.aarch64 libedit-3.1-50.20230828cvs.fc40.aarch64 libedit-devel-3.1-50.20230828cvs.fc40.aarch64 libffi-devel-3.4.4-7.fc40.aarch64 libgfortran-14.0.1-0.4.fc40.aarch64 libglvnd-1:1.7.0-4.fc40.aarch64 libglvnd-core-devel-1:1.7.0-4.fc40.aarch64 libglvnd-devel-1:1.7.0-4.fc40.aarch64 libglvnd-egl-1:1.7.0-4.fc40.aarch64 libglvnd-gles-1:1.7.0-4.fc40.aarch64 libglvnd-glx-1:1.7.0-4.fc40.aarch64 libglvnd-opengl-1:1.7.0-4.fc40.aarch64 libicu-73.2-5.fc40.aarch64 libicu-devel-73.2-5.fc40.aarch64 libjpeg-turbo-2.1.4-6.fc40.aarch64 liblerc-4.0.0-6.fc40.aarch64 libmng-2.0.3-21.fc40.aarch64 libmount-devel-2.39.3-4.fc40.aarch64 libmpc-1.3.1-5.fc40.aarch64 libpng-2:1.6.40-3.fc40.aarch64 libpng-devel-2:1.6.40-3.fc40.aarch64 libselinux-devel-3.6-4.fc40.aarch64 libsepol-devel-3.6-3.fc40.aarch64 libstdc++-devel-14.0.1-0.4.fc40.aarch64 libstdc++-static-14.0.1-0.4.fc40.aarch64 libtiff-4.6.0-2.fc40.aarch64 libubsan-14.0.1-0.4.fc40.aarch64 libuuid-devel-2.39.3-4.fc40.aarch64 libuv-1:1.47.0-6.fc40.aarch64 libwayland-client-1.22.0-3.fc40.aarch64 libwayland-server-1.22.0-3.fc40.aarch64 libwebp-1.3.2-4.fc40.aarch64 libxcb-1.16-4.fc40.aarch64 libxcb-devel-1.16-4.fc40.aarch64 libxcrypt-devel-4.4.36-5.fc40.aarch64 libxml2-devel-2.12.4-3.fc40.aarch64 libxshmfence-1.3.2-3.fc40.aarch64 llvm-17.0.6-5.fc40.aarch64 llvm-devel-17.0.6-5.fc40.aarch64 llvm-googletest-17.0.6-5.fc40.aarch64 llvm-libs-17.0.6-5.fc40.aarch64 llvm-static-17.0.6-5.fc40.aarch64 llvm-test-17.0.6-5.fc40.aarch64 make-1:4.4.1-6.fc40.aarch64 mesa-libEGL-24.0.0~rc2-5.fc40.aarch64 mesa-libGL-24.0.0~rc2-5.fc40.aarch64 mesa-libGLU-9.0.3-4.fc40.aarch64 mesa-libGLU-devel-9.0.3-4.fc40.aarch64 mesa-libgbm-24.0.0~rc2-5.fc40.aarch64 mesa-libglapi-24.0.0~rc2-5.fc40.aarch64 mpdecimal-2.5.1-9.fc40.aarch64 ncurses-c++-libs-6.4-11.20240113.fc40.aarch64 ncurses-devel-6.4-11.20240113.fc40.aarch64 nettle-3.9.1-6.fc40.aarch64 openblas-0.3.26-1.fc40.aarch64 openblas-openmp-0.3.26-1.fc40.aarch64 pcre2-devel-10.42-2.fc40.2.aarch64 pcre2-utf16-10.42-2.fc40.2.aarch64 pcre2-utf32-10.42-2.fc40.2.aarch64 pixman-0.43.0-3.fc40.aarch64 pyproject-rpm-macros-1.12.0-1.fc40.noarch python-pip-wheel-23.3.2-1.fc40.noarch python-rpm-macros-3.12-7.fc40.noarch python3-3.12.1-4.fc40.aarch64 python3-devel-3.12.1-4.fc40.aarch64 python3-libs-3.12.1-4.fc40.aarch64 python3-numpy-1:1.26.2-4.fc40.aarch64 python3-packaging-23.2-4.fc40.noarch python3-rpm-generators-14-10.fc40.noarch python3-rpm-macros-3.12-7.fc40.noarch qt-1:4.8.7-76.fc40.aarch64 qt-common-1:4.8.7-76.fc40.noarch qt-devel-1:4.8.7-76.fc40.aarch64 qt-settings-39.1-5.fc40.noarch qt-x11-1:4.8.7-76.fc40.aarch64 rhash-1.4.3-4.fc40.aarch64 sysprof-capture-devel-45.1-2.fc40.aarch64 tzdata-2023d-3.fc40.noarch vim-filesystem-2:9.1.031-2.fc40.noarch xml-common-0.6.3-63.fc40.noarch xorg-x11-proto-devel-2023.2-4.fc40.noarch xz-devel-5.4.6-1.fc40.aarch64 zlib-ng-compat-devel-2.1.6-2.fc40.aarch64 Complete! Finish: build setup for seqan2-2.4.0-22.fc40.src.rpm Start: rpmbuild seqan2-2.4.0-22.fc40.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1706486400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.9m9I4d + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf seqan-seqan-v2.4.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/seqan-seqan-v2.4.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd seqan-seqan-v2.4.0 + rm -rf /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan-disable_stripping.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan2-set_config_filepath.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/seqan2-set_awk_installation.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + find . -perm /755 -type f '(' -name '*.cpp' -o -name '*.h' ')' -exec chmod -x '{}' ';' ++ ls apps/ ++ grep -v CMakeLists + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/alf/LICENSE apps/alf/alf-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/bs_tools/LICENSE apps/bs_tools/bs_tools-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/dfi/LICENSE apps/dfi/dfi-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/fiona/LICENSE apps/fiona/fiona-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/fx_tools/LICENSE apps/fx_tools/fx_tools-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/gustaf/LICENSE apps/gustaf/gustaf-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/insegt/LICENSE apps/insegt/insegt-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/mason2/LICENSE apps/mason2/mason2-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/micro_razers/LICENSE apps/micro_razers/micro_razers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/ngs_roi/LICENSE apps/ngs_roi/ngs_roi-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/pair_align/LICENSE apps/pair_align/pair_align-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/param_chooser/LICENSE apps/param_chooser/param_chooser-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/rabema/LICENSE apps/rabema/rabema-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/razers/LICENSE apps/razers/razers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/razers3/LICENSE apps/razers3/razers3-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/rep_sep/LICENSE apps/rep_sep/rep_sep-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sak/LICENSE apps/sak/sak-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sam2matrix/LICENSE apps/sam2matrix/sam2matrix-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/samcat/LICENSE apps/samcat/samcat-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/searchjoin/LICENSE apps/searchjoin/searchjoin-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/seqan_tcoffee/LICENSE apps/seqan_tcoffee/seqan_tcoffee-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/seqcons2/LICENSE apps/seqcons2/seqcons2-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/sgip/LICENSE apps/sgip/sgip-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/snp_store/LICENSE apps/snp_store/snp_store-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/splazers/LICENSE apps/splazers/splazers-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/stellar/LICENSE apps/stellar/stellar-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/tree_recon/LICENSE apps/tree_recon/tree_recon-LICENSE + for appID in `ls apps/ | grep -v CMakeLists` + cp -p apps/yara/LICENSE apps/yara/yara-LICENSE + cp -p apps/rabema/COPYING apps/rabema/rabema-COPYING + rm -rf util/py_lib/seqan/dox/tpl/lib/font-awesome/css util/py_lib/seqan/dox/tpl/lib/font-awesome/fonts util/py_lib/seqan/dox/tpl/lib/font-awesome/less util/py_lib/seqan/dox/tpl/lib/font-awesome/scss + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.5URZBS + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-seqan-v2.4.0 + mkdir -p build/library + pushd build/library ~/build/BUILD/seqan-seqan-v2.4.0/build/library ~/build/BUILD/seqan-seqan-v2.4.0 + SEQAN_OPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG' -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/seqan2 -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/seqan2 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_LIBRARY -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON -DZLIB_INCLUDE_DIR:PATH=/usr/include -DZLIB_LIBRARY:FILEPATH=/usr/lib64/libz.so -DBZIP2_INCLUDE_DIR:PATH=/usr/include -DBZIP2_LIBRARY:FILEPATH=/usr/lib64/libbz2.so -DBoost_INCLUDE_DIR:PATH=/usr/include -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DSPHINX_EXECUTABLE:FILEPATH=/usr/bin/sphinx-build -DSPHINX_MAN_OUTPUT:BOOL=ON -DSPHINX_TEXT_OUTPUT:BOOL=ON -DYARA_LARGE_CONTIGS:BOOL=OFF ../.. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.0.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Initializing SeqAn Build System... -- Selected repository dir: /builddir/build/BUILD/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring dox CMake Deprecation Warning at dox/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Warning (dev) at dox/CMakeLists.txt:18 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "2.7") -- You need Python 2.x for building dox. (skip the tests) -- Configuring done (0.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: BUILD_SHARED_LIBS BZIP2_INCLUDE_DIR BZIP2_LIBRARY Boost_INCLUDE_DIR CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH CMAKE_SKIP_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SPHINX_EXECUTABLE SPHINX_MAN_OUTPUT SPHINX_TEXT_OUTPUT YARA_LARGE_CONTIGS ZLIB_INCLUDE_DIR ZLIB_LIBRARY -- Build files have been written to: /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library + /usr/bin/make -O -j4 V=1 VERBOSE=1 /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Nothing to be done for 'all'. /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles 0 + popd ~/build/BUILD/seqan-seqan-v2.4.0 + mkdir -p build/Release + pushd build/Release ~/build/BUILD/seqan-seqan-v2.4.0/build/Release ~/build/BUILD/seqan-seqan-v2.4.0 + SEQAN_OPT_FLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG' -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_DOCDIR:STRING=share/doc/seqan2 -DCMAKE_INSTALL_INCLUDEDIR:PATH=include/seqan2 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE -DSEQAN_BUILD_SYSTEM:STRING=SEQAN_RELEASE_APPS -DSEQAN_DISABLE_VERSION_CHECK:BOOL=ON -DZLIB_INCLUDE_DIR:PATH=/usr/include -DZLIB_LIBRARY:FILEPATH=/usr/lib64/libz.so -DBZIP2_INCLUDE_DIR:PATH=/usr/include -DBZIP2_LIBRARY:FILEPATH=/usr/lib64/libbz2.so -DBoost_INCLUDE_DIR:PATH=/usr/include -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -DYARA_LARGE_CONTIGS:BOOL=OFF -DSPHINX_EXECUTABLE:FILEPATH=/usr/bin/sphinx-build -DSPHINX_MAN_OUTPUT:BOOL=ON -DSPHINX_TEXT_OUTPUT:BOOL=ON ../.. CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is GNU 14.0.1 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:16 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Initializing SeqAn Build System... -- Selected repository dir: /builddir/build/BUILD/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps CMake Deprecation Warning at apps/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. CMake Deprecation Warning at apps/alf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/alf -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/bs_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib64/libz.so (found version "1.3.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/bs_tools/CMakeLists.txt:123 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.12.1", minimum required is "2.7") CMake Deprecation Warning at apps/dfi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/dfi -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/dfi/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fiona/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/fiona -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/fiona/CMakeLists.txt:100 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/fx_tools/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/fx_tools -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/gustaf/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/gustaf -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/gustaf/CMakeLists.txt:97 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/insegt/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/insegt -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/insegt/CMakeLists.txt:88 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/mason2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/mason2 -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/mason2/CMakeLists.txt:167 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/micro_razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/micro_razers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/micro_razers/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/ngs_roi/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/ngs_roi -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/ngs_roi/CMakeLists.txt:118 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/pair_align/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/pair_align -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/pair_align/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/param_chooser/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/param_chooser -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/rabema/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/rabema -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/rabema/CMakeLists.txt:110 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/razers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers/CMakeLists.txt:90 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/razers3/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/razers3 -- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:112 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/razers3/CMakeLists.txt:113 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/rep_sep/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/rep_sep -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Deprecation Warning at apps/sak/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sak -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sak/CMakeLists.txt:86 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sam2matrix/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sam2matrix -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sam2matrix/CMakeLists.txt:74 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/samcat/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/samcat -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/samcat/CMakeLists.txt:81 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/searchjoin/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/searchjoin -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/searchjoin/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqan_tcoffee/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/seqan_tcoffee -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqan_tcoffee/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/seqcons2/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/seqcons2 -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/seqcons2/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/sgip/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/sgip -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/sgip/CMakeLists.txt:80 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/snp_store/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/snp_store -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/snp_store/CMakeLists.txt:89 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/splazers/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/splazers -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/splazers/CMakeLists.txt:87 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/stellar/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/stellar -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/stellar/CMakeLists.txt:79 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/tree_recon/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/tree_recon -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/tree_recon/CMakeLists.txt:73 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. CMake Deprecation Warning at apps/yara/CMakeLists.txt:9 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Configuring apps/yara -- Found Seqan: /builddir/build/BUILD/seqan-seqan-v2.4.0/include (found version "2.4.0") CMake Warning (dev) at util/cmake/SeqAnBuildSystem.cmake:380 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): apps/yara/CMakeLists.txt:150 (seqan_add_app_test) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done (2.2s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_SKIP_INSTALL_RPATH INCLUDE_INSTALL_DIR LIB_INSTALL_DIR LIB_SUFFIX SPHINX_EXECUTABLE SPHINX_MAN_OUTPUT SPHINX_TEXT_OUTPUT -- Build files have been written to: /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release + make -O -j1 /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles/seqan_library.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target seqan_library make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Building CXX object apps/alf/CMakeFiles/alf.dir/alf.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/alf/CMakeFiles/alf.dir/alf.cpp.o -MF CMakeFiles/alf.dir/alf.cpp.o.d -o CMakeFiles/alf.dir/alf.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/statistics.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h: In instantiation of ‘void seqan::_alignmentFreeComparison(Matrix&, const TStringSet&, const AFScore >&) [with TValue = double; TStringSet = StringSet, Alloc<> > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/alignment_free_comparison.h:101:29: required from ‘void seqan::alignmentFreeComparison(Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = StringSet, Alloc<> > >; TValue = double; TComparisonMethod = AFScore >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 101 | _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:188:32: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 188 | alignmentFreeComparison(myMatrix, mySequenceSet, myScoreN2); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/alignment_free/af_n2.h:189:64: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); | ^ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf.cpp:164:13: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | open(seqFile, toCString(inFile)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 0%] Linking CXX executable ../../bin/alf cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf && /usr/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/alf.dir/alf.cpp.o -o ../../bin/alf -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target alf make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Building CXX object apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o -MF CMakeFiles/bisar.dir/bisar.cpp.o.d -o CMakeFiles/bisar.dir/bisar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_score.h:28:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 28 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1168:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1168 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:157:26: required from ‘int reAlign4(TReadGaps&, TContigGaps&, TFragmentStore&, TId&, TBsScoreCTLeft&, TBsScoreCTRight&, TBsScoreGALeft&, TBsScoreGARight&, TOptions&) [with TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TFragmentStore = seqan::FragmentStore; TId = unsigned int; TBsScoreCTLeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreCTRight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGALeft = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TBsScoreGARight = seqan::Score, seqan::Tag, seqan::Tag, seqan::Tag > >; TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 157 | else if (*itR == *itC || (*itR == 'T' && *itC == 'C')) ++matches; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:1168:17: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1168 | reAlign4(readGaps, contigGaps, store, id, scoringSchemeCTLeft, scoringSchemeCTRight, scoringSchemeGALeft, scoringSchemeGARight, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar_base.h:21:14: required from ‘bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 21 | if (!open(seqFileIn, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.h:996:27: required from ‘bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | loadReadsCroppedId(store, options.readFileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bisar.cpp:294:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 294 | postProcessMain(options, BsNonSimple()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 1%] Linking CXX executable ../../bin/bisar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/bisar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bisar.dir/bisar.cpp.o -o ../../bin/bisar -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Built target bisar make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Building CXX object apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -MF CMakeFiles/casbar.dir/casbar.cpp.o.d -o CMakeFiles/casbar.dir/casbar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:6, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_score.h:42:57: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct FunctorDna5OrdValueComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:17:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 17 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:66:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 66 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:81:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 81 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:129:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 129 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:142:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 142 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:165:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 165 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:184:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 184 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_realignment.h:206:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:873:31: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 873 | seqan::VcfFileOut vcfFileOut(toCString(tempFileNameVcf)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bed_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:899:31: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 899 | seqan::BedFileOut bedFileOut(toCString(tempFileNameBed)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1618:57: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1618 | TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1355:36: required from ‘void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1355 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:755:36: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 755 | doSnpAndMethCalling(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, false, vcfFileOut, bedFileOut, methOptions, options); //bs /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = SnpStoreSpec_; TConfig = FragmentStoreConfig; TContigId = int; TPos = long int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:1163:31: required from ‘void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = long int; TSetContigAnchorGaps = seqan::String, seqan::Alloc<> >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1163 | printAlignment(std::cout, layout, fragStoreGroup, 0, (TContigPos)(maxPos-100), (TContigPos)maxPos, 0, 150); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:742:35: required from ‘bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 742 | doCheckRealignCall(fragmentStoreTmp, startCoord, currentWindowBegin, currentWindowEnd, setContigAnchorGaps, vcfFileOut, bedFileOut, methOptions, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:901:32: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 901 | detectSNPsForContig(vcfFileOut, bedFileOut, fragmentStore1, currContigId, bamFileIns, records, contigIntervals, options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = SnpStoreSpec_; TFSConfig = FragmentStoreConfig; TFileNames = StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:792:16: required from ‘int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 792 | loadContigs(fragmentStore1, genomeFileNameList); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.cpp:1265:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1265 | int result = detectSNPs(options, methOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar.h:554:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readMatchesFromSamBam, seqan::Alloc >, seqan::Alloc >, seqan::FormattedFile, seqan::Tag, void>, seqan::FragmentStore >, int, long, SNPCallingOptions>(seqan::String, seqan::Alloc >, seqan::Alloc >&, seqan::FormattedFile, seqan::Tag, void>&, seqan::BamAlignmentRecord&, seqan::FragmentStore >&, seqan::FragmentStore >&, int, long, long, SNPCallingOptions&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 3%] Linking CXX executable ../../bin/casbar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/casbar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/casbar.dir/casbar.cpp.o -o ../../bin/casbar -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:937:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:351:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:352:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:353:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:354:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:437:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:361:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:362:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:363:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:364:22, inlined from ‘adjustConstantsSize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:374:24, inlined from ‘constructConstantsAndLHoods’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:518:36, inlined from ‘getCandidateProbs’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/casbar_calling.h:945:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘getCandidateProbs’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 3%] Built target casbar make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o -MF CMakeFiles/four2three.dir/four2three.cpp.o.d -o CMakeFiles/four2three.dir/four2three.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:14:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 14 | struct ConvertCT : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:23:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 23 | struct ConvertGA : public ::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:42:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | seqan::SeqFileOut seqFileOut(toCString(options.outputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.h:41:23: required from ‘bool preProcess(TOptions&) [with TOptions = AppOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | seqan::SeqFileIn seqFileIn(toCString(options.inputFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/four2three.cpp:146:15: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | preProcess(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/four2three cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/four2three.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/four2three.dir/four2three.cpp.o -o ../../bin/four2three -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target four2three make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -MF CMakeFiles/dfi.dir/dfi.cpp.o.d -o CMakeFiles/dfi.dir/dfi.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:268:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 268 | struct LessSubstringEnd : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:292:27: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 292 | struct LessRange : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:309:25: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 309 | struct LessLex : public binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:248:12: required from ‘bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | if (!open(seqFile, toCString(fileNames[s]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:498:19: required from ‘int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 498 | if (!loadDatasets(mySet, fileNames, ds)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi.cpp:835:68: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 835 | case 0: return runDFI (getArgumentValues(parser, 0), options.minFreq, options.maxFreq, options.maximal, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 4%] Linking CXX executable ../../bin/dfi cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi && /usr/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/dfi.dir/dfi.cpp.o -o ../../bin/dfi -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target dfi make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/compute_gain.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Building CXX object apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/compute_gain.dir/compute_gain.cpp.o -MF CMakeFiles/compute_gain.dir/compute_gain.cpp.o.d -o CMakeFiles/compute_gain.dir/compute_gain.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:2: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:907:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 907 | success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = Stats*; TParam = Stats]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Stats*; TParam = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = Stats*; TSource1 = Stats*; TSource2 = Stats*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = Stats]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: required from ‘typename seqan::Size >::Type seqan::reserve(String&, TSize_, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1697 | _reserveStorage(seq, new_capacity, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45: required from ‘static typename seqan::Size::Type seqan::_Resize_String::resize_(T&, typename seqan::Size::Type) [with T = seqan::String; TExpand = seqan::Tag; typename seqan::Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1725 | TSize new_capacity = reserve(me, new_length, TExpand()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50: required from ‘typename seqan::Size >::Type seqan::resize(String&, TSize, Tag) [with TValue = Stats; TSpec = Alloc<>; TSize = int; TExpand = TagGenerous_; typename Size >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1785 | return _Resize_String >::resize_(me, new_length); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18: required from ‘typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = String&; TSize = int; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1149 | return resize(std::forward(me), new_length, typename DefaultOverflowExplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:986:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | resize(stats, options.numThreads); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:98:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 98 | struct Stats | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:98:8: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> > >::Align(const seqan::Align, seqan::Alloc<> > >&)’ is deprecated [-Wdeprecated-copy] 98 | struct Stats | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> > >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/compute_gain.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘Stats::Stats(Stats&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 6%] Linking CXX executable ../../bin/compute_gain cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/compute_gain.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/compute_gain.dir/compute_gain.cpp.o -o ../../bin/compute_gain -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 6%] Built target compute_gain make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Building CXX object apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona.dir/fiona.cpp.o -MF CMakeFiles/fiona.dir/fiona.cpp.o.d -o CMakeFiles/fiona.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:81: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:118: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1636:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1636 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1654:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1654 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4410:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4410 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 82 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4412:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4412 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2259:22: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2259 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1660 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1655 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3475:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3475 | goNext(iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5002:23: required from ‘int writeOutput(unsigned int&, const TFragmentStore&, const FionaOptions&) [with TFragmentStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5002 | success = open(outFile, toCString(options.outputFilename)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5611:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5611 | int res = writeOutput(numCorrected, store, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/math/distributions.hpp:18, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:133: /usr/include/boost/math/distributions/binomial.hpp: In instantiation of ‘const std::pair<_FIter, _FIter> boost::math::support(const binomial_distribution&) [with RealType = double; Policy = policies::policy]’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: required from ‘typename Dist::value_type boost::math::detail::do_inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, typename Dist::value_type, const typename Dist::value_type&, typename Dist::value_type, const Tolerance&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; Tolerance = boost::math::tools::equal_floor; typename Dist::value_type = double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 95 | boost::math::tie(min_bound, max_bound) = support(dist); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~ /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:416:63: required from ‘typename Dist::value_type boost::math::detail::inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, const typename Dist::value_type&, const typename Dist::value_type&, const typename Dist::value_type&, const boost::math::policies::discrete_quantile&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; typename Dist::value_type = double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 416 | return round_to_floor(dist, do_inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 417 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 418 | p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~ 419 | c, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~ 420 | (guess < 1 ? value_type(1) : (value_type)floor(guess)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 421 | multiplier, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~ 422 | adder, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~ 423 | tools::equal_floor(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 424 | max_iter), p, c); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:261:49: required from ‘RealType boost::math::binomial_detail::quantile_imp(const boost::math::binomial_distribution&, const RealType&, const RealType&, bool) [with RealType = double; Policy = boost::math::policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 261 | return detail::inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 262 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 263 | comp ? q : p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ 264 | comp, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 265 | guess, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~ 266 | factor, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~ 267 | RealType(1), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~ 268 | discrete_quantile_type(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | max_iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:654:46: required from ‘RealType boost::math::quantile(const binomial_distribution&, const RealType&) [with RealType = double; Policy = policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 654 | return binomial_detail::quantile_imp(dist, p, RealType(1-p), false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/detail/derived_accessors.hpp:136:19: required from ‘typename Distribution::value_type boost::math::quantile(const Distribution&, const RealType&) [with Distribution = binomial_distribution<>; RealType = float; typename Distribution::value_type = double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 136 | return quantile(dist, static_cast(x)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3452:64: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3452 | unsigned maxAcceptedMismatches = _max((unsigned) ceil(quantile(Nmismatch, pNeig)), 2u); //unlikely that 2 reads share the same error (weese:) don't understand the comment /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 428 | const std::pair support(const binomial_distribution& dist) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 633 | else handler2->end(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 904 | writer->end(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 786 | endWrite(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 218 | struct Pipe< TInput, Multi > /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 726 | return indexCreate(index, fibre); // and create table /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 195 | indexRequire(index, FibreSA()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 211 | _indexRequireTopDownIteration(_index); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 349 | TBase(_index) {} /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /usr/include/boost/math/distributions/beta.hpp:29, from /usr/include/boost/math/distributions.hpp:17: /usr/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = long double; result_type = std::pair]’: /usr/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = long double; typename detail::fraction_traits::result_type = long double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | value_type v = g(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~^~ /usr/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = long double; typename detail::fraction_traits::result_type = long double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 156 | return continued_fraction_b(g, factor, max_terms); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:732:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 732 | T fract = boost::math::tools::continued_fraction_b(f, boost::math::policies::get_epsilon()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1377:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1377 | fract = ibeta_fraction2(a, b, x, y, pol, normalised, p_derivative); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1414:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1414 | return ibeta_imp(a, b, x, pol, inv, normalised, static_cast(nullptr)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1570:93: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/boost/math/distributions/binomial.hpp:261:49: required from ‘RealType boost::math::binomial_detail::quantile_imp(const boost::math::binomial_distribution&, const RealType&, const RealType&, bool) [with RealType = double; Policy = boost::math::policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 261 | return detail::inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 262 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~ 263 | comp ? q : p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~ 264 | comp, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~ 265 | guess, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~ 266 | factor, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~ 267 | RealType(1), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~ 268 | discrete_quantile_type(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | max_iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:654:46: required from ‘RealType boost::math::quantile(const binomial_distribution&, const RealType&) [with RealType = double; Policy = policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 654 | return binomial_detail::quantile_imp(dist, p, RealType(1-p), false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/detail/derived_accessors.hpp:136:19: required from ‘typename Distribution::value_type boost::math::quantile(const Distribution&, const RealType&) [with Distribution = binomial_distribution<>; RealType = float; typename Distribution::value_type = double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 136 | return quantile(dist, static_cast(x)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3452:64: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 3452 | unsigned maxAcceptedMismatches = _max((unsigned) ceil(quantile(Nmismatch, pNeig)), 2u); //unlikely that 2 reads share the same error (weese:) don't understand the comment /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 695 | result_type operator()() | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 881 | writer->push(Val_); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 1167 | me.push(Val_); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 414 | if (r >= 6) push(out6, o6); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 350 | _skew7ExtendMulti( /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 294 | process(_textIn); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 726 | return indexCreate(index, fibre); // and create table /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 195 | indexRequire(index, FibreSA()); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 211 | _indexRequireTopDownIteration(_index); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 349 | TBase(_index) {} /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /usr/include/boost/math/distributions/binomial.hpp:86: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp: In function ‘typename Dist::value_type boost::math::detail::do_inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, typename Dist::value_type, const typename Dist::value_type&, typename Dist::value_type, const Tolerance&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; Tolerance = boost::math::tools::equal_floor]’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | boost::math::tie(min_bound, max_bound) = support(dist); | ~~~~~~~^~~~~~ In file included from /usr/include/boost/math/special_functions/gamma.hpp:18, from /usr/include/boost/math/special_functions/beta.hpp:15: /usr/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /usr/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ In file included from /usr/include/boost/math/special_functions/detail/bernoulli_details.hpp:11, from /usr/include/boost/math/special_functions/bernoulli.hpp:16, from /usr/include/boost/math/special_functions/gamma.hpp:35: /usr/include/boost/math/tools/toms748_solve.hpp: In function ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::tools::toms748_solve(F, const T&, const T&, const T&, const T&, Tol, uintmax_t&, const Policy&) [with F = boost::math::detail::distribution_quantile_finder >; T = double; Tol = equal_floor; Policy = boost::math::policies::policy]’: /usr/include/boost/math/tools/toms748_solve.hpp:296:17: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 296 | std::pair toms748_solve(F f, const T& ax, const T& bx, const T& fax, const T& fbx, Tol tol, std::uintmax_t& max_iter, const Policy& pol) | ^~~~~~~~~~~~~ /usr/include/boost/math/tools/fraction.hpp: In function ‘boost::math::tools::continued_fraction_a, long double>(boost::math::detail::upper_incomplete_gamma_fract&, long double const&, unsigned long&)boost::math::tools::detail::fraction_traits >::result_type’: /usr/include/boost/math/tools/fraction.hpp:217:20: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ~^~ /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp: In function ‘boost::math::detail::do_inverse_discrete_quantile >, boost::math::tools::equal_floor>(boost::math::binomial_distribution > const&, boost::math::binomial_distribution >::value_type const&, bool, boost::math::binomial_distribution >::value_type, boost::math::binomial_distribution >::value_type const&, boost::math::binomial_distribution >::value_type, boost::math::tools::equal_floor const&, unsigned long&)boost::math::binomial_distribution >::value_type’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | boost::math::tie(min_bound, max_bound) = support(dist); | ~~~~~~~^~~~~~ [ 7%] Linking CXX executable ../../bin/fiona cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fiona.dir/fiona.cpp.o -o ../../bin/fiona -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextRightImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2272:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextRightImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /usr/include/boost/math/distributions/binomial.hpp: In function ‘toms748_solve’: /usr/include/boost/math/distributions/binomial.hpp:199:16: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 199 | RealType quantile_imp(const binomial_distribution& dist, const RealType& p, const RealType& q, bool comp) | ^ In function ‘continued_fraction_b’, inlined from ‘continued_fraction_b’ at /usr/include/boost/math/tools/fraction.hpp:156:31, inlined from ‘ibeta_fraction2’ at /usr/include/boost/math/special_functions/beta.hpp:732:54, inlined from ‘ibeta_imp.constprop’ at /usr/include/boost/math/special_functions/beta.hpp:1383:33: /usr/include/boost/math/tools/fraction.hpp:123:20: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 123 | value_type v = g(); | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Built target fiona make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Building CXX object apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/g++ -DFIONA_ILLUMINA -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fiona/CMakeFiles/fiona_illumina.dir/fiona.cpp.o -MF CMakeFiles/fiona_illumina.dir/fiona.cpp.o.d -o CMakeFiles/fiona_illumina.dir/fiona.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:117: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:81: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:118: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1636:34: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1636 | struct LessOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:1654:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1654 | struct LessPositionOverlap : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp: In function ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4410:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 4410 | if (options.verbosity >= 1) | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 82 | #define SEQAN_PROTIMESTART(a) _proFloat a = sysTime() | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4412:9: note: in expansion of macro ‘SEQAN_PROTIMESTART’ 4412 | SEQAN_PROTIMESTART(search); | ^~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/profiling.h:82:41: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:115: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4635:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4635 | appendValue(prefixes, infix(store.readSeqStore[i], 0, length(store.readSeqStore[i]) - cutLength)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2259:22: required from ‘void seqan::goNextImpl(Iter > > >&, VSTreeIteratorTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = Preorder; THideEmptyEdges = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2259 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19: required from ‘void seqan::goNext(Iter >&, TTraits) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >; TTraits = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1660 | goNextImpl(it, traits); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15: required from ‘void seqan::goNext(Iter >&) [with TIndex = Index, Alloc<> >, Owner<> >, IndexSa<> >; TSpec = TopDown >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1655 | goNext(it, typename GetVSTreeIteratorTraits< Iter > >::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3475:19: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3475 | goNext(iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3574:32: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 3574 | appendValue(correctCandidates, getOccurrences(iterSibling)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >*>, seqan::InfixSegment>*; TParam = seqan::Segment >*>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >*>, InfixSegment>*; TParam = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >*>, seqan::InfixSegment>, seqan::Array<4> >; TValue = seqan::Segment >*>, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >*>, InfixSegment>; TTargetSpec = Array<4>; TValue = Segment >*>, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >*>, InfixSegment>, Array<4> >&; TSource = Segment >*>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3582:24: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3582 | appendValue(correctCandidates, thickestBranchOccs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >*>, seqan::InfixSegment>::Segment(const seqan::Segment >*>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >*>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::Range >*>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5002:23: required from ‘int writeOutput(unsigned int&, const TFragmentStore&, const FionaOptions&) [with TFragmentStore = seqan::FragmentStore]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5002 | success = open(outFile, toCString(options.outputFilename)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5611:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 5611 | int res = writeOutput(numCorrected, store, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:578:18: required from ‘bool seqan::loadReadsNoNames(FragmentStore&, TFileName&, const FionaOptions&) [with TFSSpec = void; TFSConfig = FionaStoreConfig; TFileName = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 578 | if (!open(seqFile, toCString(fileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5438:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5438 | if (!loadReadsNoNames(store, options.inputFilename, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /usr/include/boost/math/distributions.hpp:18, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:133: /usr/include/boost/math/distributions/binomial.hpp: In instantiation of ‘const std::pair<_FIter, _FIter> boost::math::support(const binomial_distribution&) [with RealType = double; Policy = policies::policy]’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: required from ‘typename Dist::value_type boost::math::detail::do_inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, typename Dist::value_type, const typename Dist::value_type&, typename Dist::value_type, const Tolerance&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; Tolerance = boost::math::tools::equal_floor; typename Dist::value_type = double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 95 | boost::math::tie(min_bound, max_bound) = support(dist); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~ /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:416:63: required from ‘typename Dist::value_type boost::math::detail::inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, const typename Dist::value_type&, const typename Dist::value_type&, const typename Dist::value_type&, const boost::math::policies::discrete_quantile&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; typename Dist::value_type = double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 416 | return round_to_floor(dist, do_inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 417 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 418 | p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~ 419 | c, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~ 420 | (guess < 1 ? value_type(1) : (value_type)floor(guess)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 421 | multiplier, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~ 422 | adder, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~ 423 | tools::equal_floor(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 424 | max_iter), p, c); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:261:49: required from ‘RealType boost::math::binomial_detail::quantile_imp(const boost::math::binomial_distribution&, const RealType&, const RealType&, bool) [with RealType = double; Policy = boost::math::policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 261 | return detail::inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 262 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 263 | comp ? q : p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ 264 | comp, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~ 265 | guess, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~ 266 | factor, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~ 267 | RealType(1), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~ 268 | discrete_quantile_type(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | max_iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:654:46: required from ‘RealType boost::math::quantile(const binomial_distribution&, const RealType&) [with RealType = double; Policy = policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 654 | return binomial_detail::quantile_imp(dist, p, RealType(1-p), false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/detail/derived_accessors.hpp:136:19: required from ‘typename Distribution::value_type boost::math::quantile(const Distribution&, const RealType&) [with Distribution = binomial_distribution<>; RealType = float; typename Distribution::value_type = double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 136 | return quantile(dist, static_cast(x)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3452:64: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3452 | unsigned maxAcceptedMismatches = _max((unsigned) ceil(quantile(Nmismatch, pNeig)), 2u); //unlikely that 2 reads share the same error (weese:) don't understand the comment /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 428 | const std::pair support(const binomial_distribution& dist) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 633 | else handler2->end(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 904 | writer->end(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 786 | endWrite(); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = Range >*>; TString = String, Alloc<> >; TSpec = Owner<>; TAlgSpec = Skew7]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 218 | struct Pipe< TInput, Multi > /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = Range >*>; TSequence = String, Alloc<> >; TSetSpec = Owner<>; TAlgSpec = Skew7]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 726 | return indexCreate(index, fibre); // and create table /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 195 | indexRequire(index, FibreSA()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 211 | _indexRequireTopDownIteration(_index); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 349 | TBase(_index) {} /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /usr/include/boost/math/distributions/binomial.hpp:428:43: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /usr/include/boost/math/distributions/binomial.hpp:428:43: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /usr/include/boost/math/distributions/beta.hpp:29, from /usr/include/boost/math/distributions.hpp:17: /usr/include/boost/math/special_functions/beta.hpp: In instantiation of ‘boost::math::detail::ibeta_fraction2_t::result_type boost::math::detail::ibeta_fraction2_t::operator()() [with T = long double; result_type = std::pair]’: /usr/include/boost/math/tools/fraction.hpp:123:20: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = long double; typename detail::fraction_traits::result_type = long double; uintmax_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | value_type v = g(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~^~ /usr/include/boost/math/tools/fraction.hpp:156:31: required from ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_b(Gen&, const U&) [with Gen = boost::math::detail::ibeta_fraction2_t; U = long double; typename detail::fraction_traits::result_type = long double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 156 | return continued_fraction_b(g, factor, max_terms); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:732:54: required from ‘T boost::math::detail::ibeta_fraction2(T, T, T, T, const Policy&, bool, T*) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 732 | T fract = boost::math::tools::continued_fraction_b(f, boost::math::policies::get_epsilon()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1377:36: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool, T*) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1377 | fract = ibeta_fraction2(a, b, x, y, pol, normalised, p_derivative); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1414:20: required from ‘T boost::math::detail::ibeta_imp(T, T, T, const Policy&, bool, bool) [with T = long double; Policy = boost::math::policies::policy, boost::math::policies::promote_double, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1414 | return ibeta_imp(a, b, x, pol, inv, normalised, static_cast(nullptr)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:1570:93: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /usr/include/boost/math/distributions/binomial.hpp:261:49: required from ‘RealType boost::math::binomial_detail::quantile_imp(const boost::math::binomial_distribution&, const RealType&, const RealType&, bool) [with RealType = double; Policy = boost::math::policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 261 | return detail::inverse_discrete_quantile( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 262 | dist, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~ 263 | comp ? q : p, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~ 264 | comp, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~ 265 | guess, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~ 266 | factor, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~ 267 | RealType(1), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~ 268 | discrete_quantile_type(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~ 269 | max_iter); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~ /usr/include/boost/math/distributions/binomial.hpp:654:46: required from ‘RealType boost::math::quantile(const binomial_distribution&, const RealType&) [with RealType = double; Policy = policies::policy]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 654 | return binomial_detail::quantile_imp(dist, p, RealType(1-p), false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/distributions/detail/derived_accessors.hpp:136:19: required from ‘typename Distribution::value_type boost::math::quantile(const Distribution&, const RealType&) [with Distribution = binomial_distribution<>; RealType = float; typename Distribution::value_type = double]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 136 | return quantile(dist, static_cast(x)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:3452:64: required from ‘void traverseAndSearchCorrections(TTreeIterator, TFragmentStore&, seqan::String&, seqan::String&, FionaOptions&, seqan::Tag, unsigned int, FionaResources&) [with int LOOP_LEVEL = -1; TTreeIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >, seqan::VSTree > > >; TFragmentStore = seqan::FragmentStore; TCorrections = CorrectionIndelPos; TValueId = unsigned int; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 3452 | unsigned maxAcceptedMismatches = _max((unsigned) ceil(quantile(Nmismatch, pNeig)), 2u); //unlikely that 2 reads share the same error (weese:) don't understand the comment /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4893:41: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4893 | traverseAndSearchCorrections<-1>(myConstrainedIterator, store, correctionList, firstCorrectionForRead, options, alg, maxReadLength, resources); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 695 | result_type operator()() | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 881 | writer->push(Val_); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 1167 | me.push(Val_); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 414 | if (r >= 6) push(out6, o6); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 350 | _skew7ExtendMulti( /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 294 | process(_textIn); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 726 | return indexCreate(index, fibre); // and create table /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 195 | indexRequire(index, FibreSA()); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 211 | _indexRequireTopDownIteration(_index); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 349 | TBase(_index) {} /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /usr/include/boost/math/special_functions/beta.hpp:695:16: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /usr/include/boost/math/special_functions/beta.hpp:695:16: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Owner<> > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc<> >, Owner<> >; TSpec = IndexSa<>; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc<> >, Owner<> >; TIndexSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:349:25: required from ‘seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexSa<> >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 349 | TBase(_index) {} /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:4874:24: required from ‘unsigned int correctReads(TFragmentStore&, FionaOptions&, seqan::Tag) [with TFragmentStore = seqan::FragmentStore; TAlgorithm = FionaPoisson_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 4874 | TConstrainedIterator myConstrainedIterator(myIndex); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona.cpp:5533:44: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 5533 | numCorrected = correctReads(store, options, FionaPoisson()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /usr/include/boost/math/distributions/binomial.hpp:86: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp: In function ‘typename Dist::value_type boost::math::detail::do_inverse_discrete_quantile(const Dist&, const typename Dist::value_type&, bool, typename Dist::value_type, const typename Dist::value_type&, typename Dist::value_type, const Tolerance&, uintmax_t&) [with Dist = boost::math::binomial_distribution<>; Tolerance = boost::math::tools::equal_floor]’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | boost::math::tie(min_bound, max_bound) = support(dist); | ~~~~~~~^~~~~~ In file included from /usr/include/boost/math/special_functions/gamma.hpp:18, from /usr/include/boost/math/special_functions/beta.hpp:15: /usr/include/boost/math/tools/fraction.hpp: In function ‘typename boost::math::tools::detail::fraction_traits::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract; U = long double]’: /usr/include/boost/math/tools/fraction.hpp:217:15: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ^ In file included from /usr/include/boost/math/special_functions/detail/bernoulli_details.hpp:11, from /usr/include/boost/math/special_functions/bernoulli.hpp:16, from /usr/include/boost/math/special_functions/gamma.hpp:35: /usr/include/boost/math/tools/toms748_solve.hpp: In function ‘std::pair<_ForwardIterator, _ForwardIterator> boost::math::tools::toms748_solve(F, const T&, const T&, const T&, const T&, Tol, uintmax_t&, const Policy&) [with F = boost::math::detail::distribution_quantile_finder >; T = double; Tol = equal_floor; Policy = boost::math::policies::policy]’: /usr/include/boost/math/tools/toms748_solve.hpp:296:17: note: parameter passing for argument of type ‘std::pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 296 | std::pair toms748_solve(F f, const T& ax, const T& bx, const T& fax, const T& fbx, Tol tol, std::uintmax_t& max_iter, const Policy& pol) | ^~~~~~~~~~~~~ /usr/include/boost/math/tools/fraction.hpp: In function ‘boost::math::tools::continued_fraction_a, long double>(boost::math::detail::upper_incomplete_gamma_fract&, long double const&, unsigned long&)boost::math::tools::detail::fraction_traits >::result_type’: /usr/include/boost/math/tools/fraction.hpp:217:20: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 217 | value_type v = g(); | ~^~ /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp: In function ‘boost::math::detail::do_inverse_discrete_quantile >, boost::math::tools::equal_floor>(boost::math::binomial_distribution > const&, boost::math::binomial_distribution >::value_type const&, bool, boost::math::binomial_distribution >::value_type, boost::math::binomial_distribution >::value_type const&, boost::math::binomial_distribution >::value_type, boost::math::tools::equal_floor const&, unsigned long&)boost::math::binomial_distribution >::value_type’: /usr/include/boost/math/distributions/detail/inv_discrete_quantile.hpp:95:52: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 95 | boost::math::tie(min_bound, max_bound) = support(dist); | ~~~~~~~^~~~~~ [ 9%] Linking CXX executable ../../bin/fiona_illumina cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona && /usr/bin/cmake -E cmake_link_script CMakeFiles/fiona_illumina.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fiona_illumina.dir/fiona.cpp.o -o ../../bin/fiona_illumina -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘continued_fraction_b’, inlined from ‘continued_fraction_b’ at /usr/include/boost/math/tools/fraction.hpp:156:31, inlined from ‘ibeta_fraction2’ at /usr/include/boost/math/special_functions/beta.hpp:732:54, inlined from ‘ibeta_imp.constprop’ at /usr/include/boost/math/special_functions/beta.hpp:1383:33: /usr/include/boost/math/tools/fraction.hpp:123:20: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 123 | value_type v = g(); | ^ /usr/include/boost/math/distributions/binomial.hpp: In function ‘toms748_solve’: /usr/include/boost/math/distributions/binomial.hpp:199:16: note: parameter passing for argument of type ‘struct pair’ when C++17 is enabled changed to match C++14 in GCC 10.1 199 | RealType quantile_imp(const binomial_distribution& dist, const RealType& p, const RealType& q, bool comp) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:617:18, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextRightImpl.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2272:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘goNextRightImpl.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Built target fiona_illumina make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Building CXX object apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -MF CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o.d -o CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | if (!open(bamFile, toCString(options.inBamPath))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:254:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 254 | if (!open(bamFile, toCString(options.inBamPath))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_bam_coverage.cpp:266:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 10%] Linking CXX executable ../../bin/fx_bam_coverage cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_bam_coverage.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -o ../../bin/fx_bam_coverage -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Built target fx_bam_coverage make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Building CXX object apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -MF CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o.d -o CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_fastq_stats.cpp:290:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | if (!open(seqFile, toCString(options.inFilename))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 12%] Linking CXX executable ../../bin/fx_fastq_stats cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_fastq_stats.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -o ../../bin/fx_fastq_stats -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Built target fx_fastq_stats make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Building CXX object apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -MF CMakeFiles/gustaf.dir/gustaf.cpp.o.d -o CMakeFiles/gustaf.dir/gustaf.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:24: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seeds.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:155:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 155 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_types.h:207:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 207 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parse_lm.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/create_stellarmatches_from_file.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_parse_options.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf.cpp:25: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:1054:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, seqan::StringSet >&, seqan::StringSet&, const MSplazerOptions&, seqan::Vcf) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::Vcf = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1054 | if (!open(vcfOut, fn_vcf.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:283:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 283 | _writeGlobalBreakpoints(globalBreakpoints, databases, databaseIDs, msplazerOptions, Vcf()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:356:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, const MSplazerOptions&, seqan::Gff) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; seqan::Gff = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 356 | if (!open(gffOut, fn_gff.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:282:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 282 | _writeGlobalBreakpoints(globalBreakpoints, msplazerOptions, Gff()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:356:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, const MSplazerOptions&, seqan::Gff) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; seqan::Gff = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 356 | if (!open(gffOut, fn_gff.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:282:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 282 | _writeGlobalBreakpoints(globalBreakpoints, msplazerOptions, Gff()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_out.h:1054:14: required from ‘bool _writeGlobalBreakpoints(seqan::String&, seqan::StringSet >&, seqan::StringSet&, const MSplazerOptions&, seqan::Vcf) [with TBreakpoint = Breakpoint, seqan::Alloc<> >, seqan::String > >; TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::Vcf = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1054 | if (!open(vcfOut, fn_vcf.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:283:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 283 | _writeGlobalBreakpoints(globalBreakpoints, databases, databaseIDs, msplazerOptions, Vcf()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:190: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:801:19: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 801 | integrateAlign(align, localAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TVertexDescriptor = unsigned int; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1532:18: required from ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1532 | findIntervals(result, g, pm, act_knot, query_begin, query_end); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1513:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1513 | findIntervals(result, tree.g, tree.pm, query_begin, query_end); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:255:18: required from ‘bool _checkRightMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | findIntervals(confMateMatches, gustafChain.rightMateTree, mateIntervalBegin, mateIntervalEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:294:42: required from ‘bool _checkMateMatches(const TMatch&, const seqan::String&, const TMSplazerChain&, const MSplazerOptions&) [with TMatch = StellarMatch, seqan::Alloc<> >, seqan::String > >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 294 | return _checkRightMateMatches(sMatch, queryMatches, gustafChain, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:458:35: required from ‘void _initialiseGraphMatePairs(QueryMatches >&, TId&, TMSplazerChain&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | if (!_checkMateMatches(queryMatches.matches[i], queryMatches.matches, chain, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_algorithms.h:840:42: required from ‘void _chainQueryMatches(seqan::StringSet > >&, seqan::String&, seqan::String&, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&, const MSplazerOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TScoreAlloc = seqan::String; TMSplazerChain = MSplazerChain >, unsigned int, seqan::String, SparsePropertyMap, seqan::Alloc<> >, seqan::String > >, unsigned int>, seqan::String, seqan::Alloc<> >, seqan::String > >, seqan::Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 840 | _initialiseGraphMatePairs(stellarMatches[i], queryIds[i], chain, msplazerOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:230:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 230 | _chainQueryMatches(stellarMatches, distanceScores, queryChains, queryIDs, queries, readJoinPositions, msplazerOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1562 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1575 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1598 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf_matepairs.h:143:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 143 | if (!open(leftMates, toCString(fileNameL))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:71:30: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 71 | if (!_importSequences(msplazerOptions.queryFile[0], msplazerOptions.queryFile[1], msplazerOptions.revCompl, queries, queryIDs, readJoinPositions)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:427:10: required from ‘void seqan::assignSource(Gaps >&, const TSequence2&) [with TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequence2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 427 | value(gaps._source) = source; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:697:26: required from ‘bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = long unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | _fillMatrixBestEndsLeft(matrixLeft, possibleEndsLeft, infH, infV, seed, seedOld, scoreMatrix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar_extension.h:852:22: required from ‘bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 852 | if (!_bestExtension(infixH, infixV, seed, seedOld, alignLen, alignErr, scoreMatrix, direction, minLength, eps, align)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/stellar_routines.h:197:20: required from ‘void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | stellar(swiftFinder, swiftPattern, stellarOptions.epsilon, stellarOptions.minLength, stellarOptions.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 198 | stellarOptions.disableThresh, stellarOptions.compactThresh, stellarOptions.numMatches, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 | stellarOptions.verbose, databaseIDs[i], true, stellarMatches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer_main.h:146:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 146 | _getStellarMatches(queries, databases, databaseIDs, stellarOptions, stellarMatches); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 14%] Linking CXX executable ../../bin/gustaf cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf.dir/gustaf.cpp.o -o ../../bin/gustaf -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22, inlined from ‘_goDown’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:814:22, inlined from ‘goDown’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20, inlined from ‘goNextImpl’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2256:24, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15, inlined from ‘findRepeats’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:527:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘findRepeats’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22, inlined from ‘goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2066:18, inlined from ‘goNextImpl’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2257:28, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1660:19, inlined from ‘goNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1655:15, inlined from ‘findRepeats’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:527:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘findRepeats’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘pop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:328:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/msplazer.h:328:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘_getNextBestEndPosition’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_waterman_eggert_impl.h:659:20, inlined from ‘_localAlignmentNext’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:572:42, inlined from ‘nextLocalAlignment’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35, inlined from ‘nextLocalAlignment’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30, inlined from ‘verifySwiftHit.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/../stellar/stellar.h:607:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘verifySwiftHit.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Built target gustaf make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Building CXX object apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -MF CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o.d -o CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 257 | _open(*this, fileName, openMode, True()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:330:27: required from ‘int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 330 | seqan::SeqFileOut seqFile(toCString(outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:439:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 439 | _writeSequences(options.outPaths[0], seqs, sIds, quals); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:196:26: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 196 | seqan::SeqFileIn l(toCString(fileNameL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:437:25: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 437 | _importSequences(options.inPaths[0], options.inPaths[1], options.revCompl, seqs, ids, sIds, quals, joinPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:330:27: required from ‘int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 330 | seqan::SeqFileOut seqFile(toCString(outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/join_mates.cpp:439:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 439 | _writeSequences(options.outPaths[0], seqs, sIds, quals); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 15%] Linking CXX executable ../../bin/gustaf_mate_joining cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf_mate_joining.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -o ../../bin/gustaf_mate_joining -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Built target gustaf_mate_joining make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Building CXX object apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -MF CMakeFiles/insegt.dir/insegt.cpp.o.d -o CMakeFiles/insegt.dir/insegt.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:14: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:16: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:20: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h: In instantiation of ‘void seqan::createReadCountGFF(TFile&, TReadAnnoStore&, FragmentStore&) [with TFile = std::basic_fstream; TReadAnnoStore = String >; TSpec = void; TConfig = FragmentStoreConfig]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:889:23: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 889 | createReadCountGFF(readOutput, readAnnoStore, fragStore); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 199 | ngsOverlapper(options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:75:35: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 75 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:12: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:76:38: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 76 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:100:43: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 100 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:101:46: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 101 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:134:51: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 134 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:135:54: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 135 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:169:43: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 169 | itAnnoIds = begin(getValue(itCountStore).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/create_gff.h:170:46: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 170 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h: In instantiation of ‘seqan::Iter > seqan::nodeDown(const Iter >&) [with TFragmentStore = FragmentStore<>; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:48:64: required from ‘void seqan::adjustParentEntries(FragmentStore&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 48 | getAnnotation(it).contigId = getAnnotation(nodeDown(it)).contigId; // If no child exists: nothing happens /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:851:21: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 851 | adjustParentEntries(fragStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 853 | Iter > tmp(it); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 272 | operator = (Iter const &_origin) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)’ is deprecated [-Wdeprecated-copy] 855 | return tmp; | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: because ‘seqan::Iter, seqan::AnnotationTree<> >’ has user-provided ‘const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]’ 272 | operator = (Iter const &_origin) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::getIdsForRead(TAnnoIds&, FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TIntervalTree = IntervalTree; TIntervals = String, Alloc<> >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:18: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_annotation.h:272:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:90:13: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 90 | itR = begin(ids); | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::buildAnnoCountStore(TAnnoCountStore&, FragmentStore&, TReadAnnoStore&) [with TAnnoCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:760:21: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 760 | buildAnnoCountStore(annoCountStore, fragStore, readAnnoStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:536:51: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 536 | itAnnoIds = begin(getValue(itRead).annoIds); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:537:54: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 537 | itAnnoIdsEnd = end(getValue(itRead).annoIds); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h: In instantiation of ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:191:92: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 191 | itSecTuple = begin(tempSecTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:192:95: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 192 | itSecTupleEnd = end(tempSecTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:208:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 208 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:209:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 209 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:238:76: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 238 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:239:79: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 239 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:291:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 291 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:292:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 292 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:298:68: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 298 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:299:71: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 299 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h: In instantiation of ‘void seqan::buildTupleCountStore(TTupleCountStore&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:624:22: required from ‘void seqan::getResults(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 624 | buildTupleCountStore(tupleCountStore, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:872:13: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 872 | getResults(readAnnoStore, annoCountStore, tupleCountStore, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:354:57: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 354 | itTuple = begin(tupleSet); | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:355:60: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 355 | itTupleEnd = end(tupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:384:76: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 384 | itSecTuple = begin(secTupleSet); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:385:79: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 385 | itSecTupleEnd = end(secTupleSet); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 838 | BamFileIn inSam(toCString(options.nameSAM)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h: In instantiation of ‘void seqan::create_nTuple(TStringSet&, FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TId = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:122:60: required from ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 122 | if (exact_nTuple && n <= length(annoIds)) create_nTuple(tupleSet, fragStore, annoIds, getValue(itP), n); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:69:23: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 69 | itSet = begin(tempTupleSet); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:70:26: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 70 | itSetEnd = end(tempTupleSet); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h: In instantiation of ‘void seqan::create_Tuple(TStringSet&, FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TId = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:126:41: required from ‘void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig; TReadAnnoStore = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 126 | else if (!exact_nTuple) create_Tuple(tupleSet, fragStore, annoIds, getValue(itP), n); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:761:29: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 761 | buildTupleCountStore_Fusion(tupleCountStore, tupleCountStore_Fusion, fragStore, readAnnoStore, tupelSize, exact_nTuple); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:97:20: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 97 | it = begin(tempTupleSet); | ~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/base.h:98:23: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 98 | itEnd = end(tempTupleSet); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 848 | GffFileIn inGff(toCString(options.nameGFF)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_intervaltree.h:182:18: required from ‘void seqan::findIntervalsForInterval(String&, TIntervalTree&, TInterval&, unsigned int) [with TIntervalTree = IntervalTree; TInterval = Interval; TCargo = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 182 | findIntervals(result1, intervalTree.g, intervalTree.pm, interval.i1 + offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:85:27: required from ‘void seqan::getIdsForRead(TAnnoIds&, FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = StringSet >, Owner<> >; TSpec = void; TConfig = FragmentStoreConfig; TIntervalTree = IntervalTree; TIntervals = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 85 | findIntervalsForInterval(value(itR), intervalTree, getValue(itI), offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/fusion.h:754:18: required from ‘void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = String >; TAnnoCountStore = String >; TTupleCountStore = String >; TTupleCountStore_Fusion = String >; TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 754 | getIdsForRead(ids, fragStore, *intervalTree, getValue(it).intervals, offsetInterval); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:870:20: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 870 | getResults_Fusion(readAnnoStore, annoCountStore, tupleCountStore, tupleCountStore_Fusion, fragStore, options.nTuple, options.exact_nTuple, options.offsetInterval, options.thresholdGaps, options.unknownO); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:838:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 838 | BamFileIn inSam(toCString(options.nameSAM)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:848:15: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 848 | GffFileIn inGff(toCString(options.nameGFF)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2236:27: required from ‘void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = AlignedReadStoreElement, void>*; TPos = long int; TSize = long int; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2236 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2321:40: required from ‘void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = Gaps, AnchorGaps, Alloc<> > > >; TContigGapsPW = Gaps, AnchorGaps, Alloc<> >, InfixSegment> > >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TAlignedReadIter = AlignedReadStoreElement, void>*; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2321 | _alignedReadsInsertGaps(overlappingAlignedReadsBegin1, overlappingAlignedReadsEnd1, insPos, blkLen, readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2437:31: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2437 | _twoWayMergeAlignments( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^ 2438 | contigGapsGlobal, contigGapsPW, readGaps, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2439 | firstOverlapOld, lastOverlapOld, firstOverlapNew, it, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2440 | store.readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2393:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2393 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[it->id - offsetRecord]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2394:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2394 | TReadGaps readGaps(store.readSeqStore[it->readId], it->gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/overlap_module.h:839:16: required from ‘bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 839 | readRecords(fragStore, inSam); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt.cpp:199:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 199 | ngsOverlapper(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::Tag >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 17%] Linking CXX executable ../../bin/insegt cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt && /usr/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/insegt.dir/insegt.cpp.o -o ../../bin/insegt -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 17%] Built target insegt make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 18%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -MF CMakeFiles/mason_sim.dir/external_split_merge.cpp.o.d -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:49: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.h:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/external_split_merge.cpp:171:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In member function ‘SamJoiner::_loadNext(seqan::BamAlignmentRecord&, unsigned int)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 18%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -MF CMakeFiles/mason_sim.dir/genomic_variants.cpp.o.d -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:55: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = int; TCargo = GenomicInterval]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1502 | findIntervals(result, it.g, it.pm, query); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.cpp:718:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 718 | findIntervals(intervals, svIntervalTree, svPos); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 20%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -MF CMakeFiles/mason_sim.dir/mason_options.cpp.o.d -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:51, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 20%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -MF CMakeFiles/mason_sim.dir/methylation_levels.cpp.o.d -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_options.h:53, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 21%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_454.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 21%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_base.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_base.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 23%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_genome.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.cpp:106:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 106 | if (!open(stream, filename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 23%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:56: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:56: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 193 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:193:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 193 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_illumina.cpp:264:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 264 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -MF CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o.d -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:56: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:56: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 59 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:59:25: required from ‘void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 59 | TFragIter it = begin(frag, seqan::Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_sanger.cpp:153:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | _simulateSequence(seq, rng, TRevCompFrag(holder), cigar); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -MF CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o.d -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:167:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 167 | if (!open(vcfFileIn, toCString(vcfFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.cpp:167:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 167 | if (!open(vcfFileIn, toCString(vcfFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 25%] Linking CXX static library libmason_sim.a cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 /usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o /usr/bin/ranlib libmason_sim.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Built target mason_sim make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Building CXX object apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_genome.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 26%] Linking CXX executable ../../bin/mason_genome cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../bin/mason_genome -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 26%] Built target mason_genome make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp:143:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 143 | if (!open(outStream, toCString(options.methFastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 28%] Linking CXX executable ../../bin/mason_methylation cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../bin/mason_methylation -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Built target mason_methylation make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Building CXX object apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:153:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | if (!open(outReads, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp:142:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 142 | if (!open(inFragments, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 29%] Linking CXX executable ../../bin/mason_frag_sequencing cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../bin/mason_frag_sequencing -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 29%] Built target mason_frag_sequencing make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Building CXX object apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/random:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:43: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:833:18: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 833 | if (!open(vcfFileOut, toCString(options.vcfOutFile))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Vcf_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:833:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 833 | if (!open(vcfFileOut, toCString(options.vcfOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:884:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 884 | if (!open(outSeqStream, toCString(options.fastaOutFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 31%] Linking CXX executable ../../bin/mason_variator cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../bin/mason_variator -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_simulateFromSizes’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp:369:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551504’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_simulateFromSizes’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_variator make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Building CXX object apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:43: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp:103:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 103 | if (!open(outStream, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 31%] Linking CXX executable ../../bin/mason_materializer cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_materializer.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o ../../bin/mason_materializer -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_materializer make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Building CXX object apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -MF CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o.d -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/refwrap.h:39, from /usr/include/c++/14/vector:68, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/fragment_generation.h:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:1155:18: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1155 | if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:269:34: required from ‘void seqan::_reinitArrayGaps(Gaps >&) [with TSequence = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 269 | _setLength(gaps, length(value(gaps._source))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_array.h:155:25: required from ‘seqan::Gaps >::Gaps(TSequence&) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 155 | _reinitArrayGaps(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:219:57: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 219 | seqan::Gaps gapsContig(contigInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 586 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = String, Alloc<> >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:211:31: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = Tag; TSequenceV = String, Alloc<> >; TGapsSpecV = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 211 | return globalAlignment(gapsH, gapsV, scoringScheme, alignConfig, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_simulator.cpp:228:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 228 | editDistance = globalAlignment(gapsContig, gapsRead, sScheme, alignConfig, lDiag, uDiag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 32%] Linking CXX executable ../../bin/mason_simulator cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_simulator.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o ../../bin/mason_simulator -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘appendOperation’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:379:22, inlined from ‘simulateRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:374:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘simulateRead’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘appendOperation’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:379:22, inlined from ‘simulateRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/simulate_454.cpp:379:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘simulateRead’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Built target mason_simulator make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Building CXX object apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -MF CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o.d -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/genomic_variants.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/vcf_materialization.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGff_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagGtf_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:152:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 152 | if (!open(gffFileIn, toCString(options.inputGffFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_splicing.cpp:149:22: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 149 | if (!open(seqFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:379:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:386:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 34%] Linking CXX executable ../../bin/mason_splicing cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../bin/mason_splicing -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Built target mason_splicing make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Building CXX object apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -MF CMakeFiles/mason_tests.dir/mason_tests.cpp.o.d -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason_tests.cpp:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/methylation_levels.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/sequencing.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 35%] Linking CXX executable ../../bin/mason_tests cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../bin/mason_tests -lrt -lz libmason_sim.a -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘addVertex’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Built target mason_tests make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -MF CMakeFiles/micro_razers.dir/micro_razers.cpp.o.d -o CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:25: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:643:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 643 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:672:49: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 672 | struct LessRNoEdistHLen : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:728:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:760:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:38: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobalHamming) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobalHamming = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1359:35: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1359 | return matchVerify(m,inf,rseqNo,readSet,options,MicroRNA()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: initializing argument 2 of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, const RazerSOptions&, MicroRNA) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TSpec = RazerSSpec<>]’ 1257 | Segment inf, // potential match genome region | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1257:40: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1471:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1471 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1472:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1472 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1697:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1697 | while (find(swiftFinder, swiftPattern, 0.2)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:414:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 414 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1440:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1440 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1455:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1455 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1478:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:1971:11: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:165:25: required from ‘int mapMicroRNAReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 165 | int error = mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers.cpp:551:34: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 551 | int result = mapMicroRNAReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:992:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1010:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1020:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/../razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 37%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -MF CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o.d -o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/param_tabs.cpp [ 37%] Linking CXX executable ../../bin/micro_razers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/micro_razers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/micro_razers.dir/micro_razers.cpp.o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -o ../../bin/micro_razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Built target micro_razers make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Building CXX object apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -MF CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o.d -o CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 432 | if (!open(roiFileIn, toCString(options.inputFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 432 | if (!open(roiFileIn, toCString(options.inputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 39%] Linking CXX executable ../../bin/roi_plot_thumbnails cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_plot_thumbnails.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -o ../../bin/roi_plot_thumbnails -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Built target roi_plot_thumbnails make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 40%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -MF CMakeFiles/bam2roi.dir/bam2roi.cpp.o.d -o CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:318:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 318 | if (!open(roiFileOut, toCString(options.outputFileName))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:318:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 318 | if (!open(roiFileOut, toCString(options.outputFileName))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 40%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o -MF CMakeFiles/bam2roi.dir/roi_builder.cpp.o.d -o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 42%] Linking CXX executable ../../bin/bam2roi cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam2roi.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bam2roi.dir/bam2roi.cpp.o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -o ../../bin/bam2roi -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 42%] Built target bam2roi make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 43%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -MF CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:41: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:876:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 876 | if (!open(roiFileIn, toCString(options.inputRoiFile))) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Roi_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/roi_feature_projection.cpp:876:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 876 | if (!open(roiFileIn, toCString(options.inputRoiFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:379:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io/gff_io_base.h:386:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > > >(seqan::GffRecord&, seqan::String >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 43%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:51, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_spliced.h:52: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/gff_io.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 45%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -MF CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o.d -o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bed_io.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:38: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io/roi_io_context.h:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/roi_io.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/project_interval.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ [ 45%] Linking CXX executable ../../bin/roi_feature_projection cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_feature_projection.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -o ../../bin/roi_feature_projection -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 45%] Built target roi_feature_projection make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_global_1111 make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -MF CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o.d -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lcs.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::Lcs(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_lcs make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -MF CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o.d -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_local.cpp:41:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 41 | pairAlignConfig(options, seqan::SmithWaterman(), seqan::Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_local make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0000 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0110 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0111 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_1000 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1001 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1010 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1011 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1100 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1101 make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 86 | if (!open(inFile, fileName)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 289 | _initAlignParams(options, sc, alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:86:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 86 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:184:19: required from ‘void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 184 | _loadSequences(sequenceSet, sequenceNames, seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:276:42: required from ‘void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 276 | pairwise_align(sc, seqfile, alg, low, high, banded, outfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:289:31: required from ‘void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 289 | _initAlignParams(options, sc, alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:364:52: required from ‘void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 364 | if (options.alphabet == "dna") _initScoreMatrix(options, Dna5(), alg, spec); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 68 | pairAlignConfig(options, NeedlemanWunsch(), config); \ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1110 make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -MF CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o.d -o CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Linking CXX static library libpair_align_lib.a cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/cmake -P CMakeFiles/pair_align_lib.dir/cmake_clean_target.cmake cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align_lib.dir/link.txt --verbose=1 /usr/bin/ar qc libpair_align_lib.a CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o /usr/bin/ranlib libpair_align_lib.a make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Built target pair_align_lib make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Building CXX object apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -MF CMakeFiles/pair_align.dir/pair_align.cpp.o.d -o CMakeFiles/pair_align.dir/pair_align.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:57, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align.cpp:16: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib/pair_align_lib.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Linking CXX executable ../../bin/pair_align cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/pair_align.dir/pair_align.cpp.o -o ../../bin/pair_align lib/libpair_align_lib.a -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Built target pair_align make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -MF CMakeFiles/param_chooser.dir/param_chooser.cpp.o.d -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:32: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1430 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1431:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1431 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2253:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2253 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1653:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1653 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2256:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2256 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1399:15: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1399 | TMyersFinder myersFinder(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2242:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2242 | return mapReads(matches, genomeSet, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1625:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1625 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2245:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2245 | return mapReads(matches, genomeSet, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1414 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:1437:13: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2076:18: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2076 | mapSingleReads(matches, genomeSet[gseqNo], gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2250:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2250 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:840:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2047:11: required from ‘int seqan::mapSingleReads(TMatches&, TGenomeSet&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2047 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2150:24: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = int; TSpec = RazerSSpec; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2150 | return mapSingleReads(matches, genomeSet, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:2239:19: required from ‘int seqan::mapReads(TMatches&, TGenomeSet&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TGenomeSet = StringSet, Alloc<> > >; TReadSet = StringSet, Alloc<> >, Owner > >; TReadRegions = int; TCounts = int; TSpec = RazerSSpec]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2239 | return mapReads(matches, genomeSet, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:712:13: required from ‘void seqan::makeSelectedStatsFile(TError&, ParamChooserOptions&) [with TError = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 712 | mapReads(matches, testGenome, testReads,dummy, dummy, razersOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1079:24: required from ‘bool seqan::chooseParams(RazerSOptions&, ParamChooserOptions&) [with TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1079 | makeSelectedStatsFile(errorDistribution,pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 339 | chooseParams(r_options, pm_options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:829:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:1107:20, inlined from ‘main’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser.cpp:339:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘main’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 62%] Linking CXX executable ../../bin/param_chooser cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Built target param_chooser make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -MF CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o.d -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:42: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/test_param_chooser.cpp:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:829:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:847:66: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/../splazers/paramChooser.h:857:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::parseGappedParams, std::allocator >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::__cxx11::basic_stringstream, std::allocator >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 64%] Linking CXX executable ../../bin/test_funcs_param_chooser cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Built target test_funcs_param_chooser make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -MF CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o.d -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/prepare_sam.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 65%] Linking CXX executable ../../bin/rabema_prepare_sam cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 65%] Built target rabema_prepare_sam make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -MF CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o.d -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 118 | _host(_toPointer(host)), /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:254:100: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from ‘void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 403 | Pattern pattern(read, -(int)length(read) * 40); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from ‘int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 899 | buildErrorCurvePoints(errorCurves[readId], maxError, contig, record.rID, !hasFlagRC(record), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 900 | readSeq, readId, endPos, readNameStore, options.matchN, TPatternSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_build_gold_standard.cpp:1203:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1203 | res = matchesToErrorFunction(errorCurves, readAlignmentDistances, inBam, readNameStore, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1204 | contigNames(context(inBam)), faiIndex, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 67%] Linking CXX executable ../../bin/rabema_build_gold_standard cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Built target rabema_build_gold_standard make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -MF CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o.d -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervals(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String, StorePointsOnly>, Alloc<> >; TValue = unsigned int; TCargo = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1502:18: required from ‘void seqan::findIntervals(String&, const IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1502 | findIntervals(result, it.g, it.pm, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:644:22: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 644 | findIntervals(queryResult, intervalTrees[seqId], lastPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1441 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1453 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)’ is deprecated [-Wdeprecated-copy] 1475 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode, seqan::StorePointsOnly>’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:623:51: required from ‘int benchmarkReadResult(RabemaStats&, const seqan::String&, const seqan::BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 623 | Pattern pattern(readSeq, -static_cast(length(readSeq)) * 1000); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1003:42: required from ‘int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1003 | int res = benchmarkReadResult(result, currentSamRecords, bamFileIn, currentGsiRecords, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1004 | faiIndex, refSeqs, refIdMapping, options, tagPattern, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1005 | /*pairedEnd=*/ false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema_evaluate.cpp:1401:45: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1401 | res = compareAlignedReadsToReference(result, bamFileIn, faiIndex, refSeqs, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1402 | inGsiIter, options, MyersUkkonenReads()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 68%] Linking CXX executable ../../bin/rabema_evaluate cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Built target rabema_evaluate make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -MF CMakeFiles/rabema_do_search.dir/do_search.cpp.o.d -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:8: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:3: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:105:10: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 105 | std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 118 | _host(_toPointer(host)), /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:254:100: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 254 | TModifiedString rRightInterval(infix(errorCurve, rightmostPos, offset + intervalLength)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:52: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment, InfixSegment>; typename Iterator >::Type = Iter, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:513:97: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(ModifiedString >&, Tag) [with THost = Segment, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, InfixSegment>, AdaptorIterator > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | typename Iterator, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/curve_smoothing.h:257:91: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | for (TModifiedStringIterator it = begin(rRightInterval, Standard()); it != end(rRightInterval, Standard()); ++it) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h: In instantiation of ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>; typename Reference > >::Type = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:840:14: required from ‘void seqan::setValue(Holder >&, const TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 840 | set(value(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:625:12: required from ‘seqan::ModifiedString > seqan::reverseString(THost&) [with THost = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 625 | return ModifiedString(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:212:61: required from ‘static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 212 | setHost(pattern.data_findBeginPattern, reverseString(needle_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_begin.h:330:65: required from ‘void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = Pattern, Alloc<> >, InfixSegment>, Myers >; TNeedle = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | return FindBeginImpl_::_findBeginInit(pattern, needle_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:558:19: required from ‘void seqan::_patternFirstInit(Pattern >&, TNeedle2&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 558 | _findBeginInit(pattern, needle); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:660:22: required from ‘void seqan::_reinitPattern(Pattern >&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 660 | _patternFirstInit(pattern, needle(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:255:19: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 255 | _reinitPattern(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:452:16: required from ‘seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 452 | setHost(*this, std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/find_myers_ukkonen_reads.h:94:9: required from ‘seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 94 | _wrappedPattern(infix(ndl, 0, length(ndl) - 1), score), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/do_search.cpp:27:89: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 27 | Pattern pattern(read, -static_cast(length(read))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 70%] Linking CXX executable ../../bin/rabema_do_search cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Built target rabema_do_search make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/razers.cpp.o -MF CMakeFiles/razers.dir/razers.cpp.o.d -o CMakeFiles/razers.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:696:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 696 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:728:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 728 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:760:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 760 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:221:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1717:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1717 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1471 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1471:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1471 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1472:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1472 | TReadRev readRev(readSet[rseqNo]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2279:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2279 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = String, Alloc<> >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1699:13: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1699 | while (find(swiftFinder, swiftPattern, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2282:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2282 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:622:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 622 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/outputFormat.h:722:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:232:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 232 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2268:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2268 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:375:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 375 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1666:31: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1666 | TReadSet &readSet = host(host(swiftPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2043:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2043 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2271:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2271 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1455:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1455 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1473:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1473 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:428:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 428 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1478:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1478 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:492:40: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 492 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^ 493 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2276:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2276 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:254:13: required from ‘void seqan::setHost(Pattern&, TNeedle2&&) [with TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = Myers; TNeedle2 = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 254 | setValue(_dataHost(me), std::forward(ndl)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:1971:11: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1971 | setHost(forwardPatterns[i], indexText(swiftIndex)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2206:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2206 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:394:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 394 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers_matepairs.h:777:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 777 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2203:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2203 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.h:2265:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2265 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:209:25: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers.cpp:697:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 697 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:992:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1010:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1020:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/paramChooser.h:1285:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 71%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -MF CMakeFiles/razers.dir/param_tabs.cpp.o.d -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/param_tabs.cpp [ 71%] Linking CXX executable ../../bin/razers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lrt make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 71%] Built target razers make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -MF CMakeFiles/razers3.dir/razers.cpp.o.d -o CMakeFiles/razers3.dir/razers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:57: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:63: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:34, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:127:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:83: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:265:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 265 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:321:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 321 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:366:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 366 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1348:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1351:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1351 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1356:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1356 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSPrefix; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1359:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1359 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1304:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1304 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h: In instantiation of ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode, NMatchesNone_>; CharString = String >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1307:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1307 | return dumpMatches(store, stats, readFName, options, RazerSMode, TMatchNPolicy>()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1362:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1362 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:87:30: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 87 | #define SEQAN_DO_PRAGMA(x) _Pragma(# x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_macros.h:88:31: note: in expansion of macro ‘SEQAN_DO_PRAGMA’ 88 | #define SEQAN_OMP_PRAGMA(x) SEQAN_DO_PRAGMA(omp x) | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:672:13: note: in expansion of macro ‘SEQAN_OMP_PRAGMA’ 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:745:69: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 745 | ModifiedString > quals(fragStore.readSeqStore[idCount]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:785:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 785 | success = open(options.readFile, toCString(readFileNames[0])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:85: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1662:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1662 | return _mapMatePairReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1463 | initializeThreadLocalStoragesPaired(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 358 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 399 | indexL.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 413 | indexR.shape = shape; | ~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 835 | tls.shape = shape; | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 862 | index.shape = shape; | ~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:740:27: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 740 | writeWrappedString(iter, fragStore.readSeqStore[idCount], 60); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter >, StreamIterator > >; TSequence = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:746:27: required from ‘void seqan::write(TTarget&, FragmentStore&, Amos) [with TTarget = VirtualStream >; TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; Amos = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 746 | writeWrappedString(iter, quals, 60); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1222:14: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1222 | write(file, store, Amos()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:223: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1088 | _applyFilterOptions(filterPatternL, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2081:73: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2081 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = Hamming_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2785:21: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = Hamming_; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2785 | _patternInit(filterPattern, options.errorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3026 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2896:17: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2896 | _patternInit(filterPattern, options.errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:872:28: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 872 | _applyFilterOptions(filterPattern, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1008 | initializeThreadLocalStoragesSingle(threadLocalStorages, store, splitters, shape, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3221:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3221 | return _mapSingleReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >; TShape = Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1202:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1202 | return _mapSingleReadsParallel(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2979:24: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2979 | matchVerify(verifier, infix(filterFinder), verifier.m.readId, readSet[verifier.m.readId], mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const RazerSMode&, TReadIndex&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3054 | _mapSingleReadsToContig(matches, store, contigId, filterPattern, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3146:27: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3146 | return _mapSingleReads(store, cnts, options, mode, swiftIndex, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3216:31: required from ‘int seqan::_mapSingleReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3216 | return _mapSingleReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesNone_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:296:20: required from ‘void seqan::workVerification(ThreadLocalStorage >&, Job >&, const String >&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode; THitString = String, Alloc<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 296 | matchVerify(tls.verifier, swiftInfix(value(it), contigSeq), absReadId, tls.globalStore->readSeqStore[absReadId], TRazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:751:33: required from ‘void seqan::_mapSingleReadsParallelToContig(FragmentStore&, TThreadLocalStorages&, const String >&, const TContigId&, TCounts&, char, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TContigId = unsigned int; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 751 | workVerification(tls, job, splitters); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1033:44: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1033 | _mapSingleReadsParallelToContig(store, threadLocalStorages, splitters, contigId, cnts, 'F', options, shape, mode, TFilterSpec()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1197:39: required from ‘int seqan::_mapSingleReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1197 | return _mapSingleReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2155:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2155 | TGenomeInfix origInf(inf); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2238:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2238 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2239:41: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2239 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2341:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2341 | TReadRev readRev(readPrefix); | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2342:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 2342 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = String, Alloc<> >; TSpec = AnchorGaps, Alloc<> > >; TPosition = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 513 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2067:42: required from ‘void seqan::convertMatchesToGlobalAlignment(FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TScore = Score >; TShrinkMatches = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2067 | insertGap(gaps, insPos - rBegin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1221:40: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1221 | convertMatchesToGlobalAlignment(store, scoreType, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:680:20: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 680 | TFilterFinderR filterFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3247:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3247 | return _mapMatePairReads(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:696:16: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFilterSpec = Pigeonhole; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 696 | while (find(filterFinderR, filterPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Pigeonhole]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1115 | _mapMatePairReads(matches, store, contigId, filterPatternL, filterPatternR, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3252:33: required from ‘int seqan::_mapMatePairReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3252 | return _mapMatePairReads(store, cnts, options, Shape(), mode, Pigeonhole()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:2088:30: required from ‘bool seqan::windowFindBegin(Finder >&, Pattern >&, double) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2088 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1200:29: required from ‘void seqan::_mapMatePairReadsParallel(FragmentStore&, unsigned int, TThreadLocalStorages&, const String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1200 | if (!windowFindBegin(filterFinderR, filterPatternR, tls.options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1489:38: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_; TFilterSpec = Swift > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1489 | _mapMatePairReadsParallel(store, contigId, threadLocalStorages, splitters, cnts, 'F', options, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1657:41: required from ‘int seqan::_mapMatePairReadsParallel(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TScoreMode = RazerSErrors; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1657 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 529 | _alignAndGetCigarString(cigar, md, contigInfix, readSeq, alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:534:32: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 534 | _alignAndGetCigarString(cigar, md, contigInfix, reverseComplementString(readSeq), alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:811:66: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 811 | typename Iterator::Type sIt = begin(read, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: required from ‘void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 398 | appendValue(indexText(indexL), readSetL[j]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 859 | appendValue(indexText(index), store.readSeqStore[j]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:24: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TGapAnchors = String >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >; TSpec = GapsIterator > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >, GapsIterator > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:507:35: required from ‘void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = String >; TMDString = String >; TContigInfix = Segment, Alloc<> >, InfixSegment>; TReadSeq = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 507 | TErrors mdErrors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 654 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2241:41: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2241 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 793 | if (matchVerify(verifierL, infix(genome, ((*it).i2.beginPos >= 0) ? (TSignedGPos)(*it).i2.beginPos : (TSignedGPos)0, (TSignedGPos)(*it).i2.endPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 794 | leftReadId, readSetL[matePairId], mode)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, UngappedShape<0> >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, OneGappedShape>; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:654:36: required from ‘void seqan::_mapMatePairReads(TMatches&, FragmentStore&, unsigned int, Pattern&, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TReadIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 654 | TReadSet & readSetL = host(host(filterPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:852:30: required from ‘void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = String, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Alloc<> >; TFragmentStore = FragmentStore; TSplitters = String >; TShape = const Shape, GappedShape > >; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 852 | TIndex & index = host(tls.filterPattern); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = const Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = const Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2177:16: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2177 | while (find(myersFinder, readPrefix, state, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 430 | goEnd(it, container(it)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 737 | goEnd(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesAll_; TPatternCSP = NMatchesAll_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1537 | goEnd(finder); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2245:32: required from ‘bool seqan::matchVerify(TMatchVerifier&, Segment, unsigned int, const TRead&, const RazerSMode&) [with TMatchVerifier = MatchVerifier, String, Alloc<> >, RazerSCoreOptions >, RazerSMode, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, String > >; TGenome = String, Alloc<> >; TRead = Segment, Alloc<> >, InfixSegment>; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2245 | while (find(myersFinderRev, readRev, verifier.revPatternState, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3340:37: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3340 | return _mapMatePairReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2795:64: required from ‘void seqan::_applyFilterOptions(Pattern >&, const TOptions&) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TPigeonholeSpec = void; TOptions = RazerSCoreOptions >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 2795 | std::cout << " stepsize: " << getStepSize(host(filterPattern)) << std::endl; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = const Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = const Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:2948:40: required from ‘void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFilterSpec = Swift > >; TCounts = String >; TRazerSOptions = RazerSCoreOptions >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2948 | TReadSet & readSet = indexText(host(filterPattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3343:31: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3343 | return _mapSingleReads(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 318 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 519 | class Pattern > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: note: synthesized method ‘seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)’ first required here 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Pigeonhole >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Pigeonhole >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >; TShape = Shape, OneGappedShape>; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: required from ‘bool seqan::processRead(PairedMatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 160 | FilterPatternLSetMaxErrorsWrapper wrapperL(value(filter.callback)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:962:32: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinderL = Finder, Alloc<> >, Swift > > >; TFilterFinderR = Finder, Alloc<> >, InfixSegment>, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 962 | disabled += processRead(*tls.matchFilter, it->readId / 2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_match_filter.h:251:20: required from ‘bool seqan::processRead(MatchFilter&, unsigned int) [with TOptionsSpec = RazerSSpec<>; TReadSeqSet = StringSet, Alloc<> >, Owner > >; TCallback = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 251 | limitRead(value(filter.callback), readId, newLimit - 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:466:36: required from ‘void seqan::writeBackToLocal(ThreadLocalStorage >&, String >&, bool) [with TMatches = String, Alloc<> >; TFragmentStore = FragmentStore; TFilterFinder = Finder, Alloc<> >, Swift > > >; TFilterPattern = Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >; TShape = Shape, GappedShape > >; TOptions = RazerSCoreOptions >; TCounts = String >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 466 | disabled += processRead(*tls.matchFilter, it->readId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 110 | class ThreadLocalStorage< | ^~~~~~~~~~~~~~~~~~~ 111 | MapSingleReads< | ~~~~~~~~~~~~~~~ 112 | TMatches_, | ~~~~~~~~~~ 113 | TFragmentStore, | ~~~~~~~~~~~~~~~ 114 | TFilterFinder_, | ~~~~~~~~~~~~~~~ 115 | TFilterPattern_, | ~~~~~~~~~~~~~~~~ 116 | TShape, | ~~~~~~~ 117 | TOptions, | ~~~~~~~~~ 118 | TCounts, | ~~~~~~~~ 119 | TRazerSMode> > | ~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | return convert(getValue(source)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 149 | return convertImpl(Convert(), source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Alloc<> >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = const ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >, Tag >; TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Value::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename Reference > >::Type = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from ‘typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(Convert >, T>, const Proxy&) [with THost = SimpleType; char CHAR = '-'; TSpec = Tag; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec2 = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >, Proxy >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 357 | return convert(getValue(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: required from ‘typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = ModifiedAlphabet, ModExpand<'-'> >; TSource = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; typename Convert::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 149 | return convertImpl(Convert(), source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:17: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: required from ‘typename seqan::Convert >::Type seqan::convertImpl(Convert, const Proxy&) [with TTarget = char; T = Proxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > > >; TSpec = IteratorProxy, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > > >; typename Convert >::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 151 | return convert(getValue(source)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(const ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:314:32: required from ‘typename seqan::Position > >::Type seqan::position(const ModifiedIterator >&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | return length(container(host(me))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:675:73: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 675 | sequenceEntryForScore(scoringScheme, seqV, position(seqVBegin)), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 288 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 586 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:169:56: required from ‘typename seqan::Source > > >::Type seqan::source(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 169 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:193:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(const Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps > > >; TGapAnchors = String >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 193 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:275:20: required from ‘typename seqan::GetValue > >::Type seqan::getValue(const Proxy >&) [with TIterator = Iter, Alloc<> >, InfixSegment>, AnchorGaps > > >, GapsIterator > > > >; typename GetValue > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 275 | return getValue(iter(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorEditDistance]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1210:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1210 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = ModView > >; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:30: required from ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 278 | TContainer cont(container(host(me))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:397:81: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 397 | tmpSeqH, sequenceEntryForScore(scoringScheme, container(iter), position(iter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:891:38: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorSemiGlobalGotoh]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1215:32: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazerSMode = RazerSMode; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1215 | writeAlignments(bamFile, store, func); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1301:27: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSLocal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1301 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/outputFormat.h:1345:31: required from ‘int seqan::dumpMatches(FragmentStore&, TCounts&, CharString, RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1345 | return dumpMatches(store, stats, readFName, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:257:20: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 257 | dumpMatches(store, stats, readFileNames[0], options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 318 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:318:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 318 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:889:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 889 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:924:24: required from ‘void seqan::assign(Holder >&, const Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 924 | assignValue(target_, value(source_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:150:15: required from ‘const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 150 | assign(*this, source_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:519:11: required from ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSource = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; typename DisableIf > >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 519 | class Pattern > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TValue2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3354:39: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3354 | return _mapSingleReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3422:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3422 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesAll_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3431:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3431 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSGapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3443:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3443 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >, Swift > > >, Shape, UngappedShape<0> >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Pigeonhole >, Finder, Alloc<> >, InfixSegment>, Pigeonhole >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >, Pigeonhole >, Shape, OneGappedShape>, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3376:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3376 | return _mapReads(store, cnts, options, ungapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TParam = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:511:23: required from ‘void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource1 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*; TSource2 = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 511 | valueConstruct(target_begin, std::move(*source_begin)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1055:31: required from ‘void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, False) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1055 | _arrayConstructMoveDefault(source_begin, source_end, target_begin); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:1064:31: required from ‘void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1064 | _arrayConstructMovePointer(source_begin, source_end, target_begin, typename IsSimple::Type() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1683:27: required from ‘void seqan::_reserveStorage(String&, TSize_, Tag) [with TValue = ThreadLocalStorage, Alloc<> >, FragmentStore, Finder, Alloc<> >, Swift > > >, Finder, Alloc<> >, InfixSegment>, Swift > > >, Pattern, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >, Swift > > >, Shape, GappedShape > >, RazerSCoreOptions >, String >, RazerSMode > >; TSpec = Alloc<>; TSize_ = long unsigned int; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 1683 | arrayConstructMove(old_array, old_array + seq_length, begin(seq, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3351:45: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TRazerSMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3351 | return _mapMatePairReadsParallel(store, cnts, options, shape, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3381:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TRazersMode = RazerSMode]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3381 | return _mapReads(store, cnts, options, gapped, mode); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3396:25: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&, RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>; TAlignMode = RazerSGlobal; TGapMode = RazerSUngapped; TMatchNPolicy = NMatchesNone_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3396 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:3452:33: required from ‘int seqan::_mapReads(FragmentStore&, TCounts&, RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = FragmentStoreConfig; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 3452 | return _mapReads(store, cnts, options, RazerSMode()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:235:26: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 235 | int error = _mapReads(store, stats, (RazerSCoreOptions&)options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.cpp:866:26: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: 866 | int result = mapReads(genomeFileNames, readFileNames, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 84 | class ThreadLocalStorage > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method ‘seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)’ first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:993:51, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1011:66, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::parseGappedParams >, seqan::RazerSSpec >(seqan::RazerSOptions >&, std::basic_fstream >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1021:53, inlined from ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/paramChooser.h:1286:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::chooseParams >(seqan::RazerSOptions >&, seqan::ParamChooserOptions&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 73%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -MF CMakeFiles/razers3.dir/param_tabs.cpp.o.d -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/param_tabs.cpp [ 73%] Linking CXX executable ../../bin/razers3 cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lrt -lz -lbz2 make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Built target razers3 make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -MF CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o.d -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:996:18: required from ‘bool seqan::loadContigs(FragmentStore&, const StringSet > >&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 996 | if (!open(seqFile, toCString(fileNameList[f]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1035:23: required from ‘bool seqan::loadContigs(FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1035 | return loadContigs(store, fileNames, loadSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io.h:1043:23: required from ‘bool seqan::loadContigs(FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = FragmentStoreConfig; TFileNames = char*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1043 | return loadContigs(store, fileNames, true); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/simulate_reads.cpp:120:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | if (!loadContigs(store, toCString(referenceFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 75%] Linking CXX executable ../../bin/razers3_simulate_reads cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Built target razers3_simulate_reads make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -MF CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o.d -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:5: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/fstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:1: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:6: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:34, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:845:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 845 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:862:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 862 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:896:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 896 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:934:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 934 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:968:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 968 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1009:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1009 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1046:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1046 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1087:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1087 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1130:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1130 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1174:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1174 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers.h:1218:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1218 | public std::binary_function::Type, typename Value::Type, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/quality2prob.cpp:42:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 42 | if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 76%] Linking CXX executable ../../bin/razers3_quality2prob cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Built target razers3_quality2prob make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -MF CMakeFiles/rep_sep.dir/rep_sep.cpp.o.d -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:27: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TSource = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:702:11: required from ‘void seqan::assignValue(T&, TPos, const TValue&) [with T = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; TPos = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 702 | assign(value(me, pos), _value); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/property_map_generic.h:186:16: required from ‘typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = String, AlignedReadStoreElement, void>, long unsigned int>, Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, AlignedReadStoreElement, void>, long unsigned int>; typename EnableIf >, void>::Type = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 186 | assignValue(pm, _getId(d), val); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:191:23: required from ‘GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; typename ReadGraph::TId = unsigned int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 191 | assignProperty(me.vertexCargo, vd, new_cargo); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_construction.h:82:59: required from ‘void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 82 | TGraphCargo & new_cargo = registerRead(me, _readId(value(colIter))); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:217:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 217 | construct(rgraph, candidates, fragStore, options.contig); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>&)’ is deprecated [-Wdeprecated-copy] 118 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph.h:32, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep.cpp:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:44:5: note: because ‘GraphCargo, seqan::AlignedReadStoreElement, void>, long unsigned int>’ has user-provided ‘GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = long unsigned int]’ 44 | GraphCargo(GraphCargo const& other) | ^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::PrefixSegment> >(seqan::Segment >, seqan::PrefixSegment> const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::PrefixSegment> >(unsigned int const&, seqan::Segment >, seqan::PrefixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::SuffixSegment> >(seqan::Segment >, seqan::SuffixSegment> const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::SuffixSegment> >(unsigned int const&, seqan::Segment >, seqan::SuffixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::PrefixSegment> >(seqan::Segment >, seqan::PrefixSegment> const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::PrefixSegment> >(long const&, seqan::Segment >, seqan::PrefixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast >, seqan::SuffixSegment> >(seqan::Segment >, seqan::SuffixSegment> const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast >, seqan::SuffixSegment> >(long const&, seqan::Segment >, seqan::SuffixSegment> const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 78%] Linking CXX executable ../../bin/rep_sep cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘registerRead’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_base.h:187:41, inlined from ‘construct’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rgraph_construction.h:82:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘construct’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Built target rep_sep make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sak/CMakeFiles/sak.dir/sak.cpp.o -MF CMakeFiles/sak.dir/sak.cpp.o.d -o CMakeFiles/sak.dir/sak.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/istream:40, from /usr/include/c++/14/sstream:40, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:40: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:347:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | openRes = open(outFile, toCString(options.outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:337:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 337 | openRes = open(inFile, toCString(options.inFastxPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:347:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | openRes = open(outFile, toCString(options.outPath)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 468 | writeWrappedString(target, seq, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 475 | writeWrappedString(target, qual, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:468:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 468 | writeWrappedString(target, seq, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/tokenization.h:489:23: required from ‘void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TSequence = Segment >, InfixSegment>; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 489 | TIter iter = begin(seq, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:475:23: required from ‘typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const SequenceOutputOptions&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf, Tag > > >, void>::Type = void; Fastq = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 475 | writeWrappedString(target, qual, lineLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:423:16: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const Tag&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TagSpec = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 423 | writeRecord(file.iter, meta, seq, qual, Tag(), context(file).options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:506:20: required from ‘void seqan::writeRecord(FormattedFile, Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const TagSelector&) [with TSpec = void; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 506 | writeRecord(file, meta, seq, qual, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/sequence_file.h:519:16: required from ‘typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = FormattedFile, Tag >; TIdString = String >; TSeqString = Segment, Alloc<> >, InfixSegment>; TQualString = Segment >, InfixSegment>; typename EnableIf >, IsSequence >, void>::Type = void; typename TFile::TStream = VirtualStream, std::char_traits >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 519 | writeRecord(file, meta, seq, qual, file.format); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak.cpp:424:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 424 | writeRecord(outFile, id, infix(seqCopy, infixBegin, infixEnd), infix(quals, infixBegin, infixEnd)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 79%] Linking CXX executable ../../bin/sak cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Built target sak make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -MF CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o.d -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:37: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 257 | _open(*this, fileName, openMode, True()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:173:59: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 173 | BamFileIn bamIO(toCString(options.samFileNames[i])); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:42: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:173:59: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 173 | BamFileIn bamIO(toCString(options.samFileNames[i])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = True]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:257:14: required from ‘seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 257 | _open(*this, fileName, openMode, True()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:145:60: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | SeqFileIn seqStream(toCString(options.readNameFileName)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix.cpp:181:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘_parseSamFiles(seqan::StringSet >, seqan::Owner > >&, std::map >, unsigned int, std::less > >, std::allocator > const, unsigned int> > >&, SamToGasicOptions const&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 81%] Linking CXX executable ../../bin/sam2matrix cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target sam2matrix make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -MF CMakeFiles/samcat.dir/samcat.cpp.o.d -o CMakeFiles/samcat.dir/samcat.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat.cpp:36: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord >, seqan::AdaptorIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter >, seqan::AdaptorIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord >, seqan::AdaptorIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter >, seqan::AdaptorIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 81%] Linking CXX executable ../../bin/samcat cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target samcat make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/g++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o -MF CMakeFiles/s4_search.dir/search.cpp.o.d -o CMakeFiles/s4_search.dir/search.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 282 | index(searcher); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | prepare(searcher, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:282:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 282 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:323:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | prepare(searcher, query); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 405 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 449 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:405:10: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 405 | index(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:449:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 449 | prepare(searcher, queryLong); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:536:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 536 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, Tag, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, Tag, Writer > >, Owner > >, void>, Db > >, Owner > >, Tag >, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:536:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 536 | return runSearcher(options, TDbGeo(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:150:17: required from ‘void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 150 | _writeRecord(writer, writer.db.ids[dbId], writer.query.ids[queryId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 98 | _write(*this, dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 142 | delegate(dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:98:15: required from ‘void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | _write(*this, dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:142:13: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 142 | delegate(dbId, queryId); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:810:30: required from ‘void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 810 | dbFinder.verifier(dbId, queryId, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:508:31: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 508 | return runSearcher(options, TDbDna(), Nothing(), Online(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:524:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 524 | return runSearcher(options, TDbDna(), TDbDnaSaSmall(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:544:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 544 | return runSearcher(options, TDbGeo(), TDbGeoSaHuge(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:456:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 456 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:552:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 552 | return runSearcher(options, TDbGeo(), TDbGeoSaSmall(), Parallel(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:330:12: required from ‘int runSearcher(Options&, const TText&, const TIndex&, TSpec, const seqan::Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 330 | execute(searcher); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/search.cpp:516:39: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 516 | return runSearcher(options, TDbDna(), TDbDnaSaHuge(), Parallel(), Nothing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 82%] Linking CXX executable ../../bin/s4_search cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Built target s4_search make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/g++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -MF CMakeFiles/s4_join.dir/join.cpp.o.d -o CMakeFiles/s4_join.dir/join.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/parallel/base.h:36, from /usr/include/c++/14/parallel/algobase.h:40, from /usr/include/c++/14/parallel/algorithm:36, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 264 | index(joiner); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:319:37: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 319 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Exact()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:142: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:332:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 332 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:357:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 357 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:355:10: required from ‘void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 355 | build(dbFinder.dbIndex, dbFinder.db, seqan::Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:370:37: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 370 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Exact()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:344:10: required from ‘void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 344 | build(dbFinder.dbIndex, dbFinder.db, Default()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:264:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 264 | index(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:764:19: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 764 | dbIndex.index = TIndex(db.text); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h: In instantiation of ‘void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:374:15: required from ‘void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | buildQuery(dbFinder.queryIndex, value(dbFinder.query), dbFinder.minSeedLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:279:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 279 | prepare(joiner, db); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/db.h:888:32: warning: implicitly-declared ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)’ is deprecated [-Wdeprecated-copy] 888 | dbIndex.index[seedSet] = TIndex(db.text); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: because ‘seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]’ 88 | Index(Index const & other) : | ^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:138: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:88:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_historyClear(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:311:18: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | _historyClear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 1731 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h: In instantiation of ‘void seqan::_clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2236:15: required from ‘void seqan::clear(Iter >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 2236 | _clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:312:10: required from ‘void seqan::goRoot(Iter >, VSTree >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = TopDown<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 312 | clear(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:212:19: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 212 | goRoot(*this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 293 | close(writer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:349:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index, Alloc > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet, Alloc > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet, Alloc > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder, Alloc > >, Owner > >, Index, Alloc > >, Owner > >, IndexSa > >, void, Writer, Alloc > >, Owner > >, void>, Db, Alloc > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA >’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = seqan::SimpleType]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Preorder; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:18: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h: In instantiation of ‘void seqan::_historyPush(Iter >, VSTree > >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:377:17: required from ‘bool seqan::_goDown(Iter >, VSTree > >&, VSTreeIteratorTraits) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag; TSpec = Truncated; TDfsOrder = Preorder_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 377 | _historyPush(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:1880:20: required from ‘bool seqan::goDown(Iter > >&) [with TIndex = Index > >, Owner > >, IndexSa > >; TSpec = Truncated]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1880 | if (_goDown(it, typename GetVSTreeIteratorTraits< Iter > > >::Type())) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:527:52: required from ‘bool seqan::_moveIteratorsDown(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 527 | return goDown(back(finder.textStack)) && goDown(back(finder.patternStack)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:432:27: required from ‘bool seqan::_pushState(Finder_, Index, Backtracking >&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 432 | if (_moveIteratorsDown(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find2_backtracking.h:1311:31: required from ‘void seqan::_find(Finder_, Index, Backtracking >&, TDelegate&, const TStage&) [with TText = StringSet > >, Owner > >; TTextIndexSpec = IndexSa >; TPattern = StringSet > >, Owner > >; TPatternIndexSpec = IndexSa >; TDistance = Tag; TSpec = Tag; TStage = StageInitial_; TDelegate = DbFinder > >, Owner > >, Index > >, Owner > >, IndexSa > >, void, Writer > >, Owner > >, void>, Db > >, Owner > >, void>, Tag >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1311 | if (_pushState(finder, TStage())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:611:14: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 611 | _find(finderExt, dbFinder, StageInitial_()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared ‘constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)’ is deprecated [-Wdeprecated-copy] 630 | it._parentDesc = value(it); | ~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: because ‘seqan::VertexSA’ has user-provided ‘seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = long unsigned int; TAlphabet = char]’ 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc > >, InfixSegment>; typename Iterator >::Type = Iter, Alloc > >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment, Alloc > >, InfixSegment>; TSeq2 = Segment, Alloc > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:134:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:132:10: required from ‘void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 132 | write(writer.outputIt, id1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/writer.h:197:21: required from ‘bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 197 | _writeRecord(writer, writer.db.ids[dbId], writer.db.ids[dbId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:293:10: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 293 | close(writer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:311:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 311 | return runJoiner(options, TDbDna(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter > >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment > >, InfixSegment>; typename Iterator >::Type = Iter > >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1515:66: required from ‘unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = Segment > >, InfixSegment>; TSeq2 = Segment > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1515 | typename Iterator::Type seq1Iter = begin(seq1, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:136:52: required from ‘bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 136 | TErrors errors = _computeEditDistanceBanded(text1, text2, maxErrors); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/verifier.h:78:23: required from ‘bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 78 | return _verify(*this, dbId, queryId, delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:791:30: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 791 | dbFinder.verifier(dbId1, dbId2, dbFinder.delegate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:349:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 349 | return runJoiner(options, TDbGeo(), Nothing(), Online()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String, Alloc > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String, Alloc > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, Alloc > >; TString = String > >; TSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:173:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const StringSet&, const TAlgSpec&, True) [with TSA = String >, Alloc > >; TSequence = String > >; TSetSpec = Owner >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | _createSuffixArrayPipelining(sa, s, Skew7()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc > >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TSpec = MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe > >, Source<> >, Caster >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple >, Tag >, SorterSpec >, Tuple, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple >, Tag >, MapperSpec >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:336:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 336 | return runJoiner(options, TDbDna(), TDbDnaSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:361:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 361 | return runJoiner(options, TDbGeo(), TDbGeoSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple >, Tag >, unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:374:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 374 | return runJoiner(options, TDbGeo(), TDbGeoSaSmall(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, unsigned int>, unsigned int, File > > > >, Filter >, unsigned int> > >; TNameInput = Pool >, MapperSpec >, unsigned int>, unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, unsigned int>, unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, unsigned int>, unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:726:27: required from ‘bool seqan::indexRequire(Index&, Tag) [with TText = StringSet, Alloc > >, Owner > >; TSpec = IndexSa >; TFibre = FibreSA_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 726 | return indexCreate(index, fibre); // and create table /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_stree.h:195:17: required from ‘void seqan::_indexRequireTopDownIteration(Index >&) [with TText = StringSet, Alloc > >, Owner > >; TIndexSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 195 | indexRequire(index, FibreSA()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/finder.h:605:23: required from ‘void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 605 | TTextIterator textIt(dbFinder.dbIndex.index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:286:12: required from ‘int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 286 | execute(joiner); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/join.cpp:323:41: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 323 | return runJoiner(options, TDbDna(), TDbDnaSaHuge(), Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 84%] Linking CXX executable ../../bin/s4_join cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551440’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551424’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘eraseBack’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 84%] Built target s4_join make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -MF CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o.d -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:22: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >; TScore = long unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 571 | findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph, Alloc<> >, Dependent > >, long unsigned int, Tag > >; TSequence = String, Alloc<> >; TSetSpec = Dependent >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 678 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:191:20: required from ‘void seqan::buildAlignmentGraph(String&, Graph >&, FrequencyCounting) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TStringSet = StringSet, Alloc<> >, Dependent > >; TCargo = long unsigned int; TSpec = Tag; FrequencyCounting = const Tag]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 191 | matchRefinement(matches,strSet,outGraph); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_msa.h:178:24: required from ‘void seqan::evaluateAlignment(const MsaOptions&) [with TAlphabet = SimpleType; TScore = Score, Tag > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 178 | buildAlignmentGraph(matches, g, FrequencyCounting()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:281:26: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 281 | evaluateAlignment(msaOpt); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 305 | _initMsaParams(parser, sc); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from ‘bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 46 | if (!open(inFile, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from ‘void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 66 | _loadSequences(sequenceSet, sequenceNames, msaOpt.seqfile.c_str()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from ‘void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 290 | customizedMsaAlignment(msaOpt); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:29: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _initMsaParams(parser, sc); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:140:79, inlined from ‘seqan::read, seqan::Tag, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::Score, seqan::Tag > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:155:9, inlined from ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score/score_matrix_io.h:183:9: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadScoreMatrix, seqan::Tag >(seqan::Score, seqan::Tag > >&, char const*)bool [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::read >, seqan::Fragment > >, seqan::Alloc, int, seqan::Alloc, seqan::StringSet >, seqan::Owner > > >(std::basic_ifstream >&, seqan::String > >, seqan::Alloc >&, seqan::String >&, seqan::StringSet >, seqan::Owner > > const&, seqan::Tag)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_io.h:209:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::read >, seqan::Fragment > >, seqan::Alloc, int, seqan::Alloc, seqan::StringSet >, seqan::Owner > > >(std::basic_ifstream >&, seqan::String > >, seqan::Alloc >&, seqan::String >&, seqan::StringSet >, seqan::Owner > > const&, seqan::Tag)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 85%] Linking CXX executable ../../bin/seqan_tcoffee cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Built target seqan_tcoffee make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 87%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp:37: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 87%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons_app.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:45, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/unique_ptr.h:38, from /usr/include/c++/14/memory:78, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:35: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:48: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1618:57: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1618 | TContigIterator cit = begin(contigGaps, Standard()) + (_min(alignedRead.beginPos, alignedRead.endPos) + beginPosition(readGaps)); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:87, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h: In instantiation of ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:32: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1628:55: required from ‘void seqan::_printRead(TStream&, AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_fstream; TContigGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TReadGaps = Gaps >, AnchorGaps, Alloc<> > > >; TAlignedRead = AlignedReadStoreElement, void>; TLine = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1628 | else if (convert(*cit) == convert(*it)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:1777:23: required from ‘void seqan::printAlignment(TStream&, AlignedReadLayout&, FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_fstream; TSpec = void; TConfig = FragmentStoreConfig; TContigId = unsigned int; TPos = int; TNum = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1777 | _printRead(stream, layout, contigGaps, readGaps, align, line); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:145:27: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 145 | printAlignment(out, layout, store, /*contigID=*/contigID, /*beginPos=*/0, /*endPos=*/endPos, 0, 100); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:116:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 116 | if (!open(seqFileOut, options.outputFileConsensus.c_str())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:223:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 223 | if (!open(seqFileIn, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:223: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 370 | _patternInit(filterPattern, maxErrorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 518 | indexShape(host(pattern)) = pattern.shape; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = unsigned int; TTag = Standard_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:395:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 395 | TReadGapsIter itR = iter(readGaps, windowInfo.readAliBeginPos, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 408 | std::cerr << convert(*itR2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:811:66: required from ‘void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = String, Alloc<> >; TQual = String >; TRead = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 811 | typename Iterator::Type sIt = begin(read, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:31: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:223:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 223 | if (!open(seqFileIn, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole<>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:969:48: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 969 | pattern.finderLength = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:279:37: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(TProfileString&, TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 279 | for (TReadSeqIter it = begin(store.readSeqStore[el.readId]), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1020 | _getReadAsProfile(contigProfile, contigAlignedReads[0]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:504:15: required from ‘typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 504 | return end(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:280:33: required from ‘void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(TProfileString&, TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 280 | itEnd = end(store.readSeqStore[el.readId]); it != itEnd; ++it, ++itP) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1020:13: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1020 | _getReadAsProfile(contigProfile, contigAlignedReads[0]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:408:48: required from ‘void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, TProfileString&, seqan::ExtractProfileInfo_&, TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 408 | std::cerr << convert(*itR2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1138:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1138 | _subtractReadAlignment(windowBegin, windowEnd, profilePart, info, *it, it - begin(contigAlignedReads, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = unsigned int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = unsigned int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = unsigned int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:930:19: required from ‘void seqan::AnsonMyersRealigner_::_endContig(unsigned int) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 930 | insertGaps(contigGaps, gaps[i].i1, gaps[i].i2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:697:5: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 697 | _endContig(contigID); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, BamAlignFunctorDefault&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 572 | errors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’ 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:936:80: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 936 | _fillBamSeqAndQual(record.seq, record.qual, reverseComplementString(store.readSeqStore[alignedRead.readId])); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:88:27: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 229 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | TFilterFinder filterFinder(*it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TSpec = Pigeonhole<>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:932:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole<> >; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 932 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:941:46: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Pigeonhole<> >; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 941 | finder.haystackEnd = begin(host(finder)) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:975:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double) [with THaystack = const Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 975 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:377:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | while (find(filterFinder, filterPattern, maxErrorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h: In instantiation of ‘void seqan::findIntervalsExcludeTouching(String&, const Graph&, const TPropertyMap&, TValue) [with TSpec = Directed >; TPropertyMap = String > > > >; TValue = long unsigned int; TCargo = Pair >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from ‘void seqan::matchRefinement(TAlignmentString&, StringSet&, TScore&, TOutGraph&, typename Size::Type>::Type, TAnnotation&, Tag) [with TAlignmentString = String >; TAnnotation = bool; TOutGraph = Graph, Alloc<> >, InfixSegment>, Dependent > >, unsigned int, Tag > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSetSpec = Dependent >; TScore = unsigned int; TTagSpec = TagExactRefinement_; typename Size::Type>::Type = long unsigned int; typename Value::Type = Fragment<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 571 | findIntervalsExcludeTouching(relevant_segments, gs[seq_i_pos],pms[seq_i_pos],node_i); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from ‘void seqan::matchRefinement(TFragmentString&, StringSet&, TOutGraph&) [with TFragmentString = String >; TOutGraph = Graph, Alloc<> >, InfixSegment>, Dependent > >, unsigned int, Tag > >; TSequence = Segment, Alloc<> >, InfixSegment>; TSetSpec = Dependent >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 678 | matchRefinement(matches,strSet,fake_score,ali_graph,1,anno,ExactRefinement()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, FractionalScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet, Alloc<> >, InfixSegment>, Dependent > >; TCargo = unsigned int; TSpec = Tag; FractionalScore = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 136 | matchRefinement(matches,strSet,outGraph); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:272:24: required from ‘void seqan::buildAlignmentGraph(String&, String&, Graph >&, const TScore&, ReScore) [with TFragment = Fragment<>; TSpec1 = Alloc<>; TScoreValue = int; TSpec2 = Alloc<>; TStringSet = StringSet, Alloc<> >, InfixSegment>, Dependent > >; TCargo = unsigned int; TSpec = Tag; TScore = Score >; ReScore = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 272 | buildAlignmentGraph(matches, scores, outGraph, FractionalScore() ); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:384:24: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 384 | buildAlignmentGraph(fragments, scores, inGraph, msaScoringScheme, ReScore()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1667 | act_prop = property(pm, act_knot); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1679 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared ‘seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)’ is deprecated [-Wdeprecated-copy] 1701 | next_prop = property(pm, targetVertex(it)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: because ‘seqan::IntervalTreeNode > > >’ has user-provided ‘seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]’ 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:295:23: required from ‘bool seqan::alignmentGraphToFragmentStore(TFragmentStore&, const Graph, TCargo, TSpec> >&, const Graph >&, const String >&, const String >&, unsigned int, bool) [with TFragmentStore = FragmentStore<>; TSequence = Segment, Alloc<> >, InfixSegment>; TCargo = unsigned int; TSetSpec = Dependent >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 295 | insertGaps(gaps, from - store.alignedReadStore[*itS].beginPos, fLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:427:34: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 427 | alignmentGraphToFragmentStore(store, graph, distances, component, order, numComponents, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 | /*logging=*/(options.verbosity >= 3)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:288:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h: In instantiation of ‘seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:205:12: required from ‘typename seqan::Reference > > >::Type seqan::value(Iter > >&) [with TGaps = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Reference > > >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 205 | return TProxy(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_base.h:250:17: required from ‘typename seqan::Reference >::Type seqan::operator*(Iter&) [with TContainer = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >; TSpec = GapsIterator, Alloc<> > > >; typename Reference >::Type = Proxy, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 250 | return value(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:209:39: required from ‘unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = String >; TGaps1 = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGaps2 = Gaps, Alloc<> >, InfixSegment>, ModView > > >, Tag >, AnchorGaps, Alloc<> > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 209 | if ((TVal1)*it1 == (TVal2)*it2) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/cigar.h:572:29: required from ‘void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, BamAlignFunctorDefault&) [with TCigar = String >; TMDString = String >; TContig = ContigStoreElement, Alloc<> >, GapAnchor, void>; TReadSeq = Segment, Alloc<> >, InfixSegment>; TAlignedRead = const AlignedReadStoreElement, void>; TErrors = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 572 | errors = getMDString(md, contigGaps, readGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:905:27: required from ‘void seqan::setPrimaryMatch(BamAlignmentRecord&, FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = void; TConfig = FragmentStoreConfig; TAlignedRead = AlignedReadStoreElement, void>; TAlignQuality = AlignQualityStoreElement; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 905 | alignAndGetCigarString(record.cigar, record.qual, store.contigStore[alignedRead.contigId], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 906 | store.readSeqStore[alignedRead.readId], alignedRead, errors, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1076:24: required from ‘void seqan::writeAlignments(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1076 | setPrimaryMatch(record, store, alignedRead, *alignQualityPtr, functor, secondary); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1109:20: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig; TBamIOFunctor = BamAlignFunctorDefault]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1109 | writeAlignments(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:1118:17: required from ‘void seqan::writeRecords(FormattedFile, Tag, TSpec>&, FragmentStore&) [with TSpec = void; TFSSpec = void; TFSConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1118 | writeRecords(bamFile, store, functor); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:153:21: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 153 | writeRecords(out, store); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/proxy_iterator.h:89:15: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:376:20: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 376 | appendValue(seqs, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:162:56: required from ‘typename seqan::Source > > >::Type seqan::source(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 162 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 183 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const Gaps&) [with TTarget = Iter, StreamIterator > >; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 950 | writeValue(target, convert(getValue(begin_))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const Gaps&) [with TTarget = std::basic_ostream; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 965 | write(it, gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 363 | std::cerr << "READ GAPS\t" << readGaps << "\n"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1067 | _computeReadClippingInfo(windowInfo, *it, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = int; TCount = unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:513:15: required from ‘void seqan::insertGap(Gaps&, TPosition) [with TSequence = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >; TPosition = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 513 | insertGaps(gaps, clippedViewPos, 1u); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1610:30: required from ‘void seqan::AnsonMyersRealignmentRound_::_updateAlignments(unsigned int, unsigned int&, TProfileString&, seqan::Gaps::Type>::Type>::Type> > >&, seqan::Gaps::Type>&, seqan::ExtractProfileInfo_&, const seqan::WindowClippingInfo_&, const TAlignedReadIter&) [with TFragmentStore = seqan::FragmentStore<>; TProfileString = seqan::String >, seqan::Alloc<> >; typename seqan::BaseAlphabet::Type>::Type>::Type = seqan::SimpleType; typename seqan::Value::Type>::Type = seqan::SimpleType; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename TFragmentStore::TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1610 | insertGap(anchorReadGaps, readGapsPos++); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1321:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1321 | _updateAlignments(windowBegin, windowEnd, profilePart, profileGaps, readGaps, info, windowInfo, it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:466:20: required from ‘void seqan::insertGaps(Gaps >&, TPosition, TCount) [with TSequence = Segment, Alloc<> >, InfixSegment>; TGapAnchors = String, Alloc<> >; TPosition = long int; TCount = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 466 | TIter it = iter(gaps, clippedViewPos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2236:27: required from ‘void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = AlignedReadStoreElement, void>*; TPos = long int; TSize = long int; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2236 | insertGaps(gaps, insPos - rBegin, blkLen); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2321:40: required from ‘void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = Gaps, AnchorGaps, Alloc<> > > >; TContigGapsPW = Gaps, AnchorGaps, Alloc<> >, InfixSegment> > >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TAlignedReadIter = AlignedReadStoreElement, void>*; TReadSeqStore = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2321 | _alignedReadsInsertGaps(overlappingAlignedReadsBegin1, overlappingAlignedReadsEnd1, insPos, blkLen, readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2437:31: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 2437 | _twoWayMergeAlignments( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~^ 2438 | contigGapsGlobal, contigGapsPW, readGaps, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2439 | firstOverlapOld, lastOverlapOld, firstOverlapNew, it, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2440 | store.readSeqStore); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = TagSelector, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:261:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 261 | readRecords(store, bamFileIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:229:32: required from ‘seqan::Finder >::Finder(THaystack&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 229 | data_iterator(begin(haystack, Rooted())), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:376:23: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 376 | TFilterFinder filterFinder(*it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:162:17: required from ‘typename seqan::Source > > >::Type seqan::source(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename Source > > >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 162 | return begin(source(*me.data_container), Rooted()) + me.current.seqPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:183:24: required from ‘typename seqan::GetValue > > >::Type seqan::getValue(Iter > >&) [with TGaps = const Gaps, Alloc<> >, InfixSegment>, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; typename GetValue > > >::Type = ModifiedAlphabet, ModExpand<'-'> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 183 | else return *source(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:950:54: required from ‘void seqan::write(TTarget&, const Gaps&) [with TTarget = Iter, StreamIterator > >; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 950 | writeValue(target, convert(getValue(begin_))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_base.h:965:10: required from ‘TTarget& seqan::operator<<(TTarget&, const Gaps&) [with TTarget = std::basic_ostream; TSource = Segment, Alloc<> >, InfixSegment>; TSpec = AnchorGaps, Alloc<> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 965 | write(it, gaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:363:40: required from ‘void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; TAlignedReadElement = seqan::AlignedReadStoreElement, void>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 363 | std::cerr << "READ GAPS\t" << readGaps << "\n"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1067:9: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1067 | _computeReadClippingInfo(windowInfo, *it, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:165:9: required from ‘seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 165 | data_gaps(anchors), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2393:29: required from ‘void seqan::convertPairWiseToGlobalAlignment(FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = FragmentStoreConfig; TContigGapsString = StringSet, Alloc<> >, Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2393 | TContigGapsPW contigGapsPW(/*contigInfix, */gaps[it->id - offsetRecord]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:337:41: required from ‘void seqan::readRecords(FragmentStore&, BamIOContext&, TForwardIter&, const TFormat&, const FragStoreImportFlags&) [with TSpec = void; TConfig = FragmentStoreConfig; TNameStore = StringSet > >; TNameStoreCache = NameStoreCache > > >; TStorageSpec = Dependent >; TForwardIter = Iter >, StreamIterator > >; TFormat = TagSelector, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 337 | convertPairWiseToGlobalAlignment(store, contigAnchorGaps); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:361:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&, const FragStoreImportFlags&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 361 | readRecords(store, ctx, directionIterator(bamFile, Input()), format(bamFile), importFlags); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:373:16: required from ‘void seqan::readRecords(FragmentStore&, FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = FragmentStoreConfig; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 373 | readRecords(store, bamFile, FragStoreImportFlags()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:261:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 261 | readRecords(store, bamFileIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:352:20: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 352 | appendValue(superSet, store.readSeqStore[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Pigeonhole<>; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_pigeonhole.h:463:41: required from ‘void seqan::_patternInit(Pattern >&, TFloat) [with TIndex = Index, Alloc<> >, InfixSegment>, Dependent > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 463 | TSize seqCount = countSequences(host(pattern)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:370:17: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 370 | _patternInit(filterPattern, maxErrorRate); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:334:30: required from ‘void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 334 | buildAllToAllOverlapInfos(infos, readIDs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:163:34: required from ‘void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 163 | buildAllToAllOverlapInfos(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:160:22: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 160 | ovlInfoHelper.run(overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = const seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 86 | class Index > | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: required from ‘TScoreValue seqan::globalAlignment(Align&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequence = Segment, Alloc<> >, InfixSegment>; TAlignSpec = Tag; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = true; bool RIGHT = true; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 99 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(row(align, 0)), source(row(align, 1)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 | scoringScheme, TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlapper.h:354:24: required from ‘bool seqan::Overlapper_::computeOverlap(seqan::Overlap_&, TFragments&, const TSequence&, const TSequence&, const seqan::OverlapCandidate_&) const [with TFragments = seqan::String >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 354 | globalAlignment(align, scoringScheme, alignConfig, lDiag, uDiag, Gotoh()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:138:38: required from ‘void seqan::ConsensusBuilder_::computeOverlaps(TFragments&, seqan::String&, seqan::Graph >&, const TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>; TFragments = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 138 | if (overlapper.computeOverlap(ovl, frags, store.readSeqStore[it->seq0], store.readSeqStore[it->seq1], /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 139 | OverlapCandidate_(it->seq0, it->seq1, it->pos1 - it->numErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 140 | it->pos1 + it->numErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:370:5: required from ‘void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 370 | computeOverlaps(fragments, scores, distances, store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner.h:170:20: required from ‘void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | consBuilder.run(store, overlapInfos); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from ‘void seqan::consensusAlignment(FragmentStore&, const ConsensusAlignmentOptions&) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 141 | aligner.run(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:296:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | consensusAlignment(store, caOptions); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = ConsensusScoreSequenceEntry >, Alloc<> > >; TSeqVValue = ConsensusScoreSequenceEntry, Alloc<> >, InfixSegment> >; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >, Score > > >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 382 | for (; iter != seqEnd - 1; ++iter) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = ConsensusScoreSequenceEntry >, Alloc<> > >; TSeqVValue = ConsensusScoreSequenceEntry, Alloc<> >, InfixSegment> >; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >, Score > > >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 453 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqHValue, seqVValue, seqBegin, seqEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 454 | scoringScheme, cacheDiag, cacheVert, TColumnDescriptor{}, TDPProfile{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >, Score > > >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 516 | sequenceEntryForScore(scoringScheme, seqH, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 517 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 518 | seqVBegin, seqVEnd, scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 519 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >, Score > > >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = String >, Alloc<> >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = WeightedConsensusScore >, Score > >; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:639:20: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, const TAlgoTag&) [with TProfileGaps = Gaps >, Alloc<> >, Tag >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, Tag >; TConsensusScore = Score >, Score > > >; TAlignConfig = AlignConfig; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 639 | globalAlignment(profileGaps, readGaps, consScore, alignConfig, /*lowerBand, upperBand, */tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:657:36: required from ‘void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, bool) [with TProfileGaps = Gaps >, Alloc<> >, Tag >; TReadGaps = Gaps, Alloc<> >, InfixSegment>, Tag >; TConsensusScore = Score >, Score > > >; TAlignConfig = AlignConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 657 | _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 658 | NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1209:36: required from ‘void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1209 | _readToProfileAlignment(profileGaps, readGaps, consScore, alignConfig, lowerBand, upperBand, linear); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:685:18: required from ‘void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | round.run(windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/realign/realign_base.h:1801:18: required from ‘void seqan::reAlignment(FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = FragmentStoreConfig]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1801 | realigner.run(contigID, windowBegin, windowEnd); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_app.cpp:314:20: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 314 | reAlignment(store, contigID, /*method=*/2, options.reAlignmentBandwidth, /*includeReference=*/false); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, void> >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, void> > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:231:19, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::TagList, seqan::TagList, void> > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:233:19, inlined from ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_io_sam.h:573:15: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_readOneAlignment, seqan::StringSet, seqan::Alloc >, seqan::Owner > >, seqan::String, seqan::Alloc >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent >, seqan::Iter, std::char_traits >, seqan::StreamIterator > >, seqan::TagSelector, seqan::TagList, void> > > >(seqan::FragmentStore >&, seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::String, seqan::Alloc >&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::TagSelector, seqan::TagList, void> > > const&, seqan::FragStoreSAMContext > >&, seqan::FragStoreImportFlags const&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 89%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/g++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -MF CMakeFiles/seqcons2.dir/seqcons_options.cpp.o.d -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons_options.h:39: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 89%] Linking CXX executable ../../bin/seqcons2 cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph.constprop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:164:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_copyGraph.constprop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1136:19, inlined from ‘upgmaTree’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:803:12, inlined from ‘upgmaTree’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_guidetree.h:892:14, inlined from ‘run’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_builder.h:397:14: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘run’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 89%] Built target seqcons2 make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Building CXX object apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o -MF CMakeFiles/sgip.dir/sgip.cpp.o.d -o CMakeFiles/sgip.dir/sgip.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:27: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:33, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ [ 90%] Linking CXX executable ../../bin/sgip cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../bin/sgip -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:735:43, inlined from ‘_createUndir’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:358:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createUndir’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_undirected.h:357:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:736:29, inlined from ‘_createUndir’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip_base.h:358:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createUndir’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:735:43, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:736:29, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addEdge’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:604:22, inlined from ‘addEdges’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:740:16, inlined from ‘_createGraph.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip.h:99:13: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_createGraph.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Built target sgip make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o -MF CMakeFiles/snp_store.dir/snp_store.cpp.o.d -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:32: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:31: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:33: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:35: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:88:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 88 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/consensus_library.h:99:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::unary_function >, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:53: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:356:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 356 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:405:39: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 405 | struct LessPosLen : public ::std::binary_function < TPosLen, TPosLen, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:420:23: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 420 | public ::std::binary_function < typename Value::Type, typename Value::Type, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:468:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 468 | struct LessId : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:481:37: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 481 | struct LessGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:504:40: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 504 | struct LessGPosEnd : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:523:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 523 | struct LessGPosEndOa : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:545:36: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 545 | struct HigherQ : public ::std::binary_function < TQual, TQual, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:54, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/pair_base.h: In instantiation of ‘seqan::Pair::Pair(const T1&, const T2&) [with T1 = unsigned int; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:5148:46: required from ‘void seqan::dumpShortIndelPolymorphismsBatch(TFragmentStore&, TReadCigars&, TGenome&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TGenome = String, Alloc<> >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 5148 | Pair(1,rInf))); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:971:74: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 971 | if(!options.realign) dumpShortIndelPolymorphismsBatch(fragmentStore, readCigars, fragmentStore.contigStore[0].seq, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, indelFileStream, options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 1412 | int result = detectSNPs(options); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/pair_base.h:120:53: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 120 | Pair(T1 const & _i1, T2 const & _i2) : i1(_i1), i2(_i2) {} | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_align.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:679:35: required from ‘typename seqan::Iterator >::Type seqan::iter(T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 679 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:661:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 661 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:4057:36: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4057 | TContigGapIter refIt = iter(referenceGaps,candidateViewPos-refStart); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2477 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2478 | readCounts,genomeID, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~ 2479 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2480 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h: In instantiation of ‘seqan::Iter > > seqan::operator+(const Iter > >&, TDifference) [with TGaps = const Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TGapAnchors = String, Alloc<> >; TDifference = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:689:35: required from ‘typename seqan::Iterator >::Type seqan::iter(const T&, TPos, const Tag&) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; TTag = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 689 | return begin(me, Tag()) + pos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:669:16: required from ‘typename seqan::Iterator::Type>::Type seqan::iter(const T&, TPos) [with T = Gaps, Alloc<> >, AnchorGaps, Alloc<> > > >; TPos = long int; typename Iterator::Type>::Type = Iter, Alloc<> >, AnchorGaps, Alloc<> > > >, GapsIterator, Alloc<> > > > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 669 | return iter(me, pos, typename DefaultGetIteratorSpec::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:451:22: required from ‘bool seqan::isGap(const Gaps >&, TPosition) [with TSequence = String, Alloc<> >; TGapAnchors = String, Alloc<> >; TPosition = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 451 | return isGap(iter(gaps, clippedViewPos)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:4418:72: required from ‘void seqan::dumpVariantsRealignBatch(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCounts = String >; TReadCigars = StringSet > >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 4418 | ((indelConsens[candidateViewPos].i1 & 7) == 6 && isGap(referenceGaps, candidateViewPos-refStart))) // position in consensus is the same as in reference /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.h:2477:41: required from ‘void seqan::dumpVariantsRealignBatchWrap(TFragmentStore&, TReadCigars&, const TReadCounts&, TGenomeName, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, TFile&, TFile&, TOptions&) [with TFragmentStore = FragmentStore; TReadCigars = StringSet > >; TReadCounts = String >; TGenomeName = String >; TFile = std::basic_ofstream; TOptions = SNPCallingOptions<>; typename TFragmentStore::TContigPos = long int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2477 | dumpVariantsRealignBatch(fragStoreGroup,readCigars, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2478 | readCounts,genomeID, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~ 2479 | groupStartCoord,groupStartPos,groupEndPos, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2480 | fileSNPs,fileIndels,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:986:53: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 986 | dumpVariantsRealignBatchWrap(fragmentStore, readCigars, readCounts, genomeNames[i], startCoord, currentWindowBegin, currentWindowEnd, snpFileStream,indelFileStream,options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >&)’ is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because ‘seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >, seqan::GapsIterator, seqan::Alloc<> > > > >’ has user-provided ‘const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps, seqan::Alloc<> > > >; TGapAnchors_ = seqan::String, seqan::Alloc<> >]’ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_iterator_anchor.h:112:18: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:77:18: required from ‘bool loadGenomes(TGenomeSet&, seqan::StringSet > >&, std::map >, TGenomeSetSize>&, TGenomeNames&) [with TGenomeSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TGenomeSetSize = long unsigned int; TGenomeNames = seqan::StringSet > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 77 | if (!open(seqFileIn, toCString(fileNameList[filecount]))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:670:56: required from ‘int detectSNPs(seqan::SNPCallingOptions&) [with TSpec = seqan::SNPCallingSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 670 | if(result == CALLSNPS_GENOME_FAILED || !loadGenomes(genomes, genomeFileNameList, gIdStringToIdNumMap, genomeNames)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store.cpp:1412:28: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1412 | int result = detectSNPs(options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void [clone .isra.0]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 92%] Linking CXX executable ../../bin/snp_store cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../bin/snp_store -lrt -lz In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:274:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘obtainId’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_idmanager.h:166:15, inlined from ‘addVertex’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:525:36, inlined from ‘_createVertices’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_interface.h:704:67, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:276:32, inlined from ‘_copyGraph’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:300:15, inlined from ‘__ct ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_types/graph_impl_directed.h:87:23, inlined from ‘__ct_base ’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/interval_tree.h:358:7: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551608’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘__ct_base ’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Built target snp_store make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Building CXX object apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/splazers/CMakeFiles/splazers.dir/splazers.cpp.o -MF CMakeFiles/splazers.dir/splazers.cpp.o.d -o CMakeFiles/splazers.dir/splazers.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:28, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:29: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:676:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 676 | struct LessRNoGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:704:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 704 | struct LessRNoGEndPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:730:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 730 | struct LessErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:748:41: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 748 | struct LessSplicedScore : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:770:45: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 770 | struct LessSplicedScoreGPos : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:51: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:126:44: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 126 | struct LessGPosRNo : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:513:47: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 513 | struct LessPairErrors : public ::std::binary_function < TReadMatch, TReadMatch, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h: In instantiation of ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 140 | _host(std::forward(host)), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:210:11: required from ‘bool seqan::loadReadsSam(TReadSet&, TNameSet&, TReadRegions&, const char*, TRazerSOptions&) [with TReadSet = StringSet, Alloc<> >, Owner > >; TNameSet = StringSet > >; TReadRegions = String > > >; TRazerSOptions = RazerSOptions<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 210 | if (!open(file, fileName)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:190:21: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 190 | if (!loadReadsSam(readSet, readNames, readRegions, toCString(readFileNames[0]), options)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:666:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestPrefix; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2591:20: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2591 | if (matchVerify( (*it).i2, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~ 2592 | infix(genome, (*it).i2.gBegin, maxEndPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2593 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~ 2594 | readSet, //readSetL /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~ 2595 | forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~ 2596 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~ 2597 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~ 2598 | LongestPrefix()) && /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:666:22: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 666 | TGenomeInfix oriInf = inf; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 674 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h: In instantiation of ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1658:15: required from ‘void seqan::mapSingleReads(TMatches&, TGenome&, unsigned int, Pattern >&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1658 | matchVerify(m, infix(swiftFinder), rseqNo, readSet, forwardPatterns, options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1979:19: required from ‘int seqan::mapSingleReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1979 | mapSingleReads(matches, genome, gseqNo, swiftPattern, forwardPatterns, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2125:24: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2125 | return mapSingleReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:33: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1430 | TGenomeInfixRev infRev(inf); | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:140:13: required from ‘seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void; typename seqan::RemoveReference::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; typename seqan::RemoveReference::Type = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 140 | _host(std::forward(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_shortcuts.h:340:12: required from ‘typename seqan::ReverseComplementString::Type seqan::reverseComplementString(const THost&) [with THost = Segment, Alloc<> >, InfixSegment>; typename ReverseComplementString::Type = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 340 | return TRevComp(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:40: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment, Alloc<> >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = Segment, Alloc<> >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:789:10: required from ‘TStream& seqan::operator<<(TStream&, const Segment&) [with TStream = VirtualStream >; THost = const String, Alloc<> >; TSpec = InfixSegment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 789 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:900:12: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 900 | file << reads[(*it).rseqNo]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:98:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 98 | class ModifiedIterator > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; typename Iterator >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:801:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = VirtualStream >; THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 801 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:604:11: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | if (!open(seqFile, fname) || atEnd(seqFile)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2419:16: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2419 | TSwiftFinderL swiftFinderL(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:222: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3041 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:87: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3043 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/cyclic_shape.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:68: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:674:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 674 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3074:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3074 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3076:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 3076 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:395:32: required from ‘seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 395 | data_iterator(begin(haystack, Rooted())), haystackEnd(), _needReinit(true), curHit(), endHit(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 671 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2187 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2190 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1928:77: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1928 | pattern.finderLength = pattern.params.tabooLength + length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1430:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1430 | TGenomeInfixRev infRev(inf); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2198:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2198 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h: In instantiation of ‘void seqan::_patternInit(Pattern >&, TFloat, TSize_) [with TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TFloat = double; TSize_ = int; TSpec = Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1929:21: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1929 | _patternInit(pattern, errorRate, minLength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2201:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 2201 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:752:23: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 752 | pattern.shape = indexShape(host(pattern)); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder, Alloc<> >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment, Alloc<> >, InfixSegment>; typename Haystack::Type = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 910 | return container(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1682 | int64_t textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1693 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2489 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(const Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:910:21: required from ‘typename seqan::Parameter_::Type>::Type seqan::haystack(const TObject&) [with TObject = Finder, Alloc<> >, InfixSegment>, Swift > > >; typename Parameter_::Type>::Type = Segment, Alloc<> >, InfixSegment>; typename Haystack::Type = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 910 | return container(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1682:38: required from ‘seqan::Pair > >::Type> seqan::positionRange(const Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1682 | int64_t textEnd = length(haystack(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1693:25: required from ‘seqan::Pair > >::Type> seqan::positionRange(Finder >&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Tag >; typename Position > >::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1693 | return positionRange(const_cast > const &>(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2489:26: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2489 | gPair = positionRange(swiftFinderL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:606:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 606 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:675:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 675 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1876:41: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1876 | finder.haystackEnd = begin(tmpHost) + (finder.endPos - length(pattern.shape) + 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:48: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::host(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = Swift > >; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1866:36: required from ‘bool seqan::_firstNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1866 | finder.endPos = length(host(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1934:34: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1934 | if (!_firstNonRepeatRange(finder, pattern)) return false; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:585:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 585 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:663:20: required from ‘typename seqan::Iterator, const seqan::Tag >::Type seqan::end(ModifiedString&, Tag) [with THost = const Segment, Alloc<> >, InfixSegment>; TSpec = ModView > >; TTagSpec = Rooted_; typename Iterator, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 663 | TResult tmp(end(host(me), tag_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >; typename Iterator >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, ModView > > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter >, StreamIterator > >; TContainer = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >, Tag >; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:801:10: required from ‘TStream& seqan::operator<<(TStream&, const ModifiedString&) [with TStream = VirtualStream >; THost = ModifiedString, Alloc<> >, InfixSegment>, ModView > > >; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 801 | write(it, source); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/outputFormat.h:1591:14: required from ‘void seqan::dumpMatches(TMatches&, const TGenomeNames&, StringSet > >&, std::map, unsigned int> >&, const TReads&, const TReadRegions&, TCounts&, const TReadNames&, CharString, CharString, RazerSOptions&) [with TMatches = String >; TGenomeNames = StringSet > >; TReads = StringSet, Alloc<> >, Owner > >; TReadRegions = String > > >; TReadNames = StringSet > >; TCounts = String >; TSpec = RazerSSpec<>; CharString = String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1591 | file << reverseComplementString(reads[currReadNo]) << "\t*\t"; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:281:14: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 281 | dumpMatches(matches, genomeNames, genomeFileNames, gnoToFileMap, readSet, readRegions, stats, readNames, readFileNames[0], errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2383:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2383 | TReadSetL &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2384 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, OneGappedShape>; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3041:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 3041 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, onegappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2384:33: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2384 | TReadSetR &readSetR = host(host(swiftPatternR)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, GappedShape > >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3043:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3043 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, gappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:652:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 652 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:675:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 675 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:1717:14: required from ‘bool seqan::combineLeftRight(TMatch&, TMatch&, TRead&, TGenome&, RazerSOptions&, char, SwiftSemiGlobal) [with TMatch = ReadMatch; TRead = const Segment, Alloc<> >, InfixSegment>; TGenome = String, Alloc<> >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1717 | appendValue(strL,genomeInfL); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, OneGappedShape>, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, OneGappedShape>; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2187:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 2187 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, onegapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_onegapped.h:107:9: note: because ‘seqan::Shape, seqan::OneGappedShape>’ has user-provided ‘seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]’ 107 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSource = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TValue2 = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSpec = Swift > >; typename Host >::Type = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:652:32: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, GappedShape > >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 652 | TReadSet &readSetL = host(host(swiftPatternL)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, GappedShape > >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2190:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2190 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, gapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:278:5: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >’ has user-provided ‘seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >; TSpec = seqan::Tag]’ 278 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:229:7: warning: implicitly-declared ‘seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)’ is deprecated [-Wdeprecated-copy] 229 | class Index > { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/shape_gapped.h:281:9: note: because ‘seqan::Shape, seqan::GappedShape > >’ has user-provided ‘seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]’ 281 | Shape(Shape const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method ‘seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)’ first required here 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Alloc<> >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, void>; TNeedle = String, Alloc<> >; TSpec = FindInfix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1414:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1414 | while (find(myersFinder, myersPattern, minScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1432:19: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | TMyersFinderRev myersFinderRev(infRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2454:13: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2454 | while (find(swiftFinderR, swiftPatternR, maxErrorRateR)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3039:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3039 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:688:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal, TSufPrefSpec) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TSpec = RazerSSpec<>; TSufPrefSpec = LongestSuffix; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 688 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2543:21: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2543 | if (!matchVerify(mR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~ 2544 | infix(genome,minBeginPos,endPosition(infix(swiftFinderR, genomeInf))), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2545 | rseqNo, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~ 2546 | readSet,//readSetR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~ 2547 | forwardPatternsR, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 2548 | options, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~ 2549 | TSwiftSpec(), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ 2550 | LongestSuffix())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:369:17: required from ‘typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename DefaultGetIteratorSpec::Type = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 369 | return begin(me, typename DefaultGetIteratorSpec::Type()) ; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1845:33: required from ‘bool seqan::_nextNonRepeatRange(TFinder&, Pattern >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1845 | hostIterator(finder) = begin(host(finder)) + finder.startPos; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1965:37: required from ‘bool seqan::find(Finder >&, Pattern >&, double, TSize) [with THaystack = Segment, Alloc<> >, InfixSegment>; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Tag >; TSize = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1965 | if (!_nextNonRepeatRange(finder, pattern)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/find_swift.h:1913:16: required from ‘bool seqan::find(TFinder&, Pattern > > >&, double) [with TFinder = Finder, Alloc<> >, InfixSegment>, Swift > > >; TIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSpec = Hamming_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1913 | return find(finder, pattern, errorRate, 0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:705:13: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 705 | while (find(swiftFinderR, swiftPatternR, options.errorRate)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:21: required from ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = void; typename Parameter_::Type = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 599 | return container(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1603:45: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1603 | TSize haystack_length = length(container(finder)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1636:16: required from ‘bool seqan::find(TFinder&, const Pattern >&, PatternState_ >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; THasState = True; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1636 | return find(finder, pattern, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1654:16: required from ‘bool seqan::find(TFinder&, Pattern >&, int) [with TFinder = Finder, Alloc<> >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1654 | return find(finder, pattern, pattern, minScore); //static cast /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:1437:13: required from ‘bool seqan::matchVerify(TMatch&, Segment, unsigned int, TReadSet&, TMyersPatterns&, const RazerSOptions&, SwiftSemiGlobal) [with TMatch = ReadMatch; TGenome = String, Alloc<> >; TReadSet = StringSet, Alloc<> >, Owner > >; TMyersPatterns = String, Alloc<> >, Myers > >; TSpec = RazerSSpec<>; SwiftSemiGlobal = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1437 | while (find(myersFinderRev, myersPatternRev, maxScore)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:763:21: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 763 | if (matchVerify( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^ 764 | (*it).i2, infix(genome, (*it).i2.gBegin, (*it).i2.gEnd), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 765 | rseqNo, readSetL, forwardPatternsL, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 766 | options, TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2195:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 2195 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2701:25: required from ‘void seqan::mapSplicedReads(TMatches&, TGenome&, unsigned int, TOriReadSet&, TReadRegions&, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TOriReadSet = StringSet, Alloc<> >, Owner > >; TReadIndexL = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TReadIndexR = Index, Alloc<> >, InfixSegment>, Owner<> >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, InfixSegment>, Myers >, Alloc<> >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2701 | !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:2237:20: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet_&, TReadRegions&, TCounts&, RazerSOptions&, const TShapeL&, const TShapeR&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShapeL = Shape, UngappedShape<0> >; TShapeR = Shape, UngappedShape<0> >; TSwiftSpec = Tag >; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2237 | mapSplicedReads(matches, genome, gseqNo, readSet, readRegions, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:3072:27: required from ‘int seqan::mapSplicedReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 3072 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options, ungappedL, ungappedR, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2169:31: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2169 | return mapSplicedReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, readRegions, cnts, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:259:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:671:16: required from ‘void seqan::mapMatePairReads(TMatches&, TGenome&, unsigned int, Pattern >&, Pattern >&, TVerifier&, TVerifier&, TCounts&, char, RazerSOptions&) [with TMatches = String >; TGenome = String, Alloc<> >; TReadIndex = Index, Alloc<> >, Owner > >, IndexQGram, UngappedShape<0> >, Tag > >; TSwiftSpec = Tag >; TVerifier = String, Alloc<> >, Myers > >; TCounts = String >; TSpec = RazerSSpec<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 671 | TSwiftFinderR swiftFinderR(genomeInf, options.repeatLength, 1); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_matepairs.h:1028:21: required from ‘int seqan::mapMatePairReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, const TReadSet_&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet_ = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1028 | mapMatePairReads(matches, genome, gseqNo, swiftPatternL, swiftPatternR, forwardPatternsL, forwardPatternsR, cnts, 'F', options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2122:26: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TCounts&, RazerSOptions&, const TShape&, Swift) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TShape = Shape, UngappedShape<0> >; TSwiftSpec = Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2122 | return mapMatePairReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, shape, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers.h:2184:19: required from ‘int seqan::mapReads(TMatches&, StringSet > >&, StringSet > >&, std::map, unsigned int> >&, TReadSet&, TReadRegions&, TCounts&, RazerSOptions&) [with TMatches = String >; TReadSet = StringSet, Alloc<> >, Owner > >; TCounts = String >; TSpec = RazerSSpec<>; TReadRegions = String > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 2184 | return mapReads(matches, genomeFileNameList, genomeNames, gnoToFileMap, readSet, cnts, options, ungapped, Swift()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:250:22: required from ‘int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::CharString&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 250 | int error = mapReads(matches, genomeFileNames, genomeNames, gnoToFileMap, readSet, readRegions, stats, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers.cpp:717:23: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 717 | int result = mapReads(genomeFileNames, readFileNames, errorPrbFileName, options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned int const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned short const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(unsigned char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast(char* const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, char*>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, char*>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, char*>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, char*>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, char*>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:151:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast(signed char const&, char* const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(int)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)short’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(short)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(unsigned char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:627:13, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)signed char’, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:82:21, inlined from ‘seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>::operator()(signed char)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:77:10, inlined from ‘seqan::tagApply >, seqan::String >&>, signed char>(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:620:16, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned char, seqan::TagList >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, char, seqan::TagList > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned short, seqan::TagList > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, short, seqan::TagList > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, float, seqan::TagList > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, unsigned int, seqan::TagList > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::tagApply >, seqan::String >&>, int, seqan::TagList > > > > > > >(seqan::AppendTagsSamToBamOneTagHelper_ >, seqan::String >&>&, seqan::TagList > > > > > > >)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_tags.h:629:20, inlined from ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:166:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::_appendTagsSamToBamOneTag >, seqan::Iter > const, seqan::AdaptorIterator > > >(seqan::String >&, seqan::Iter > const, seqan::AdaptorIterator > >&, seqan::String >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const signed char &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(signed char const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:277:40, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned short’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:306:44, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const short unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned short const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:320:50, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ In function ‘seqan::lexicalCast > >(seqan::String > const&)int’, inlined from ‘seqan::readRecord, std::char_traits >, seqan::StreamIterator > >, seqan::StringSet >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >(seqan::BamAlignmentRecord&, seqan::BamIOContext >, seqan::Owner > >, seqan::NameStoreCache >, seqan::Owner > >, seqan::String > >, seqan::Dependent > >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&, seqan::Tag const&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/read_sam.h:363:43, inlined from ‘seqan::readRecord(seqan::BamAlignmentRecord&, seqan::FormattedFile, seqan::Tag, void>&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:241:15, inlined from ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/razers_spliced.h:236:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘seqan::loadReadsSam, seqan::Alloc >, seqan::Owner > >, seqan::StringSet >, seqan::Owner > >, seqan::String >, void>, seqan::Alloc >, seqan::RazerSOptions > >(seqan::StringSet, seqan::Alloc >, seqan::Owner > >&, seqan::StringSet >, seqan::Owner > >&, seqan::String >, void>, seqan::Alloc >&, char const*, seqan::RazerSOptions >&)bool’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(int const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 93%] Linking CXX executable ../../bin/splazers cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers && /usr/bin/cmake -E cmake_link_script CMakeFiles/splazers.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/splazers.dir/splazers.cpp.o -o ../../bin/splazers -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toHtml’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/tool_doc.h:285:34: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551568’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘_toHtml’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Built target splazers make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Building CXX object apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o -MF CMakeFiles/stellar.dir/stellar.cpp.o.d -o CMakeFiles/stellar.dir/stellar.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:24: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:44: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:25: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:30, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:28: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_types.h:155:32: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 155 | struct LessPos : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_types.h:207:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 207 | struct LessLength : public ::std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:127:18: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public::std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /usr/include/c++/14/bits/stl_function.h:117:12: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /usr/include/c++/14/bits/stl_function.h:117:12: note: 685 | mainWithOptions(options, String()); /usr/include/c++/14/bits/stl_function.h:117:12: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:60:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 60 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | databaseID, databaseStrand, matches, BestLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:68:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 68 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | databaseID, databaseStrand, matches, BandedGlobalExtend()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:47: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 677 | Segment finderSegment(finderInfixSeq, | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:690:74: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:102:46: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:103:29: required from ‘seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Host >::Type = seqan::Segment >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 103 | data_host(_toPointer(_host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:677:33: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 677 | Segment finderSegment(finderInfixSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h: In instantiation of ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:194:24: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 194 | TAlign ali(align); | ^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:202:32: required from ‘typename seqan::Parameter_::Type seqan::host(const Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 202 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:577:88: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 577 | TScore mismatchIndel = (TScore)_max((TScore) ceil(-1/eps) + 1, -(TScore)length(host(infH))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment, Alloc<> >, InfixSegment>; typename Parameter_::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:195:32: required from ‘typename seqan::Parameter_::Type seqan::host(Segment&) [with THost_ = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:773:28: required from ‘void integrateAlign(seqan::Align&, const seqan::Align, seqan::InfixSegment>, TSpec2>&) [with TSource = seqan::String >; TSpec1 = seqan::Tag; TSpec2 = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 773 | pos += beginPosition(host(source(row(infixAlign, i)))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:467:16: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 467 | integrateAlign(align, bandedAlign); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:190: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:105: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h: In instantiation of ‘void seqan::_alignBandedSmithWatermanDeclump(LocalAlignmentFinder&, const TSequenceH&, const TSequenceV&, const TScore&, TScoreValue, TDiagonal, TDiagonal) [with TScoreValue = int; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScore = Score >; TDiagonal = int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:570:37: required from ‘TScoreValue seqan::_localAlignmentNext(LocalAlignmentFinder&, Gaps&, Gaps&, const TScore&, TScoreValue, TDiagonal, TDiagonal, const BandedWatermanEggert&) [with TScoreValue = int; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag; TScore = Score >; TDiagonal = int; BandedWatermanEggert = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 570 | _alignBandedSmithWatermanDeclump(finder, source(gapsH), source(gapsV), sc, cutoff, diag1, diag2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:109:35: required from ‘bool seqan::nextLocalAlignment(Gaps&, Gaps&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TGapsSpecH = Tag; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TGapsSpecV = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 109 | return _localAlignmentNext(enumerator._finder, gapsH, gapsV, enumerator._score, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 | enumerator._cutoff, enumerator._lowerDiag, enumerator._upperDiag, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 111 | BandedWatermanEggert()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_enumeration_banded.h:121:30: required from ‘bool seqan::nextLocalAlignment(Align&, LocalAlignmentEnumerator, Tag >&) [with TScoreValue = int; TScoreSpec = Tag; TSequence = Segment >, InfixSegment>, InfixSegment>; TAlignSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 121 | return nextLocalAlignment(row(align, 0), row(align, 1), enumerator); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:607:30: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 607 | while (nextLocalAlignment(localAlign, enumerator)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/local_alignment_banded_waterman_eggert_impl.h:287:20: warning: implicitly-declared ‘constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)’ is deprecated [-Wdeprecated-copy] 287 | matIt2 = matIt - diagonalWidth; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: because ‘seqan::Iter, seqan::CountingIteratorImpl_ > >’ has user-provided ‘seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]’ 105 | Iter(Iter const & other_) : | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:105:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:72, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSource = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index, Alloc<> >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h: In instantiation of ‘typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = Index >, Dependent > >, IndexQGram, Tag > >; TSource = Index >, Dependent > >, IndexQGram, Tag > >; typename DisableIf > >::Type = void]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:645:15: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; TValue2 = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 645 | assign(_dataValue(me), value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: required from ‘typename seqan::Reference > >::Type seqan::value(Holder >&) [with TValue = Index >, Dependent > >, IndexQGram, Tag > >; typename Reference > >::Type = Index >, Dependent > >, IndexQGram, Tag > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 863 | create(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:339:17: required from ‘typename seqan::Host >::Type& seqan::host(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Host >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 339 | return value(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_pattern_base.h:395:16: required from ‘typename seqan::Needle >::Type& seqan::needle(Pattern&) [with TNeedle = Index >, Dependent > >, IndexQGram, Tag > >; TSpec = Swift >; typename Needle >::Type = Index >, Dependent > >, IndexQGram, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 395 | return host(obj); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:687:78: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 687 | TPatternSeq patternSeq = getSequenceByNo(pattern.curSeqNo, indexText(needle(pattern))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >&)’ is deprecated [-Wdeprecated-copy] 110 | target = source; | ~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because ‘seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >’ has user-provided ‘seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]’ 143 | Index(Index const &other): | ^~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:241:14: required from ‘bool _importSequences(const seqan::CharString&, const seqan::CharString&, seqan::StringSet >&, seqan::StringSet >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 241 | if (!open(inSeqs, (toCString(fileName)))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:618:26: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 618 | if (!_importSequences(options.queryFile, "query", queries, queryIDs)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram_openaddressing.h:143:9: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String, Alloc<> >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align, Alloc<> >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align >, InfixSegment>, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Align >, InfixSegment>, InfixSegment>, Tag >*; TParam = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >, seqan::Alloc<> >; TValue = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Align >, InfixSegment>, InfixSegment>, Tag >; TTargetSpec = Alloc<>; TValue = Align >, InfixSegment>, InfixSegment>, Tag >&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = String >, InfixSegment>, InfixSegment>, Tag >, Alloc<> >&; TSource = Align >, InfixSegment>, InfixSegment>, Tag >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:217:28: required from ‘void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 217 | appendValue(alignmentString, ali); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:614:23: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 614 | _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: because ‘seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >’ has user-provided ‘seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]’ 104 | Align & operator=(Align const & other) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/align_base.h:104:13: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TValue2 = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>, InfixSegment>*; TParam = const Segment >, InfixSegment>, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder >, InfixSegment>, InfixSegment>, Tag >; TValue = Segment >, InfixSegment>, InfixSegment>; typename Value::Type = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment >, InfixSegment>, InfixSegment>; TValue2 = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:594:19: required from ‘void seqan::create(Holder >&) [with TValue = Segment >, InfixSegment>, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 594 | create(me, _dataValue(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:604:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 604 | assignSource(row(localAlign, 0), infH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h: In instantiation of ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: required from ‘void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 396 | appendValue(str, infixH); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value | ^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:744:24: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 744 | TConstSeqHIterator seqHIter = seqHIterBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment >, InfixSegment>, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment >, InfixSegment>, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter >, InfixSegment>, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:685:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 685 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:687:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 687 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:689:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 689 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:691:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 691 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment, Alloc<> >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment, Alloc<> >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment, Alloc<> >, InfixSegment>; TString2 = Segment, Alloc<> >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet, Alloc<> >, InfixSegment>, Owner<> >&; TSource = Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment, Alloc<> >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:693:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 693 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>*; TParam = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1348:31: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1348 | valueConstruct(begin(me, Standard()) + me_length, std::forward(temp_copy)); //??? this should be valueMoveConstruct /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment >, InfixSegment>*; TParam = const Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1354:27: required from ‘static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1354 | valueConstruct(begin(me, Standard()) + me_length, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1366:54: required from ‘void seqan::appendValue(String&, TValue&&, Tag) [with TTargetValue = Segment >, InfixSegment>; TTargetSpec = Alloc<>; TValue = const Segment >, InfixSegment>&; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1366 | AppendValueToString_ >::appendValue_(me, std::forward(_value)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_owner.h:174:16: required from ‘void seqan::appendValue(StringSet >&, const TString2&, Tag) [with TString = Segment >, InfixSegment>; TString2 = Segment >, InfixSegment>; TExpand = TagGenerous_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | appendValue(me.strings, obj, tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:937:16: required from ‘void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = StringSet >, InfixSegment>, Owner<> >&; TSource = Segment >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 937 | appendValue(std::forward(me), std::forward(_value), typename DefaultOverflowImplicit::Type()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:633:26: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 633 | if (!_extendAndExtract(*aliIt, scoreDropOff, scoreMatrix, infH, infV, direction, minLength, eps, align)) { /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 56 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 | databaseID, databaseStrand, matches, AllLocal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = Segment >, InfixSegment>; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: required from ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment >, InfixSegment>, InfixSegment>; TIterator = char*; TSpec = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 647 | return Iter >(container(left), hostIterator(left) - right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_<>; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_<>; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment >, InfixSegment>, InfixSegment>; TSequenceV = Segment >, InfixSegment>, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_<>; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:458:17: required from ‘void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 458 | globalAlignment(bandedAlign, scoreMatrix, lowerDiag, upperDiag, NeedlemanWunsch()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:17: required from ‘void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 705 | verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 706 | pattern.bucketParams[0].delta + pattern.bucketParams[0].overlap, disableThresh, compactThresh, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 707 | numMatches, databaseID, dbStrand, value(matches, pattern.curSeqNo), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:64:16: required from ‘bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 64 | stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 65 | options.disableThresh, options.compactThresh, options.numMatches, options.verbose, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 | databaseID, databaseStrand, matches, BandedGlobal()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:31: required from ‘bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 174 | if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:23: required from ‘int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 655 | if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 695 | mainWithOptions(options, String()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]’ 143 | operator = (Segment const & source) | ^~~~~~~~ [ 95%] Linking CXX executable ../../bin/stellar cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../bin/stellar -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551584’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘pop’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_goUp’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_wotd.h:915:22: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_goUp’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Built target stellar make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon && /usr/bin/g++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_EXECINFO=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o -MF CMakeFiles/tree_recon.dir/tree_recon.cpp.o.d -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:62, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:37, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:19: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:18: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:39: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:41: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa.h:44: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_msa/graph_align_tcoffee_base.h:304:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 304 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:119: In function ‘seqan::lexicalCast > >(seqan::String > const&)unsigned long’, inlined from ‘readPhylipMatrix >, seqan::String >, seqan::Alloc >, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::String >&, seqan::String >, seqan::Alloc >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon.cpp:54:40: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:255:9: warning: ‘target’ may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h: In function ‘readPhylipMatrix >, seqan::String >, seqan::Alloc >, seqan::Iter, std::char_traits >, seqan::StreamIterator > > >(seqan::String >&, seqan::String >, seqan::Alloc >&, seqan::Iter, std::char_traits >, seqan::StreamIterator > >&)void’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type ‘const long unsigned int &’ to ‘seqan::BadLexicalCast::BadLexicalCast > >(unsigned long const&, seqan::String > const&)’ declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/lexical_cast.h:253:13: note: ‘target’ declared here 253 | TTarget target; | ^~~~~~ [ 96%] Linking CXX executable ../../bin/tree_recon cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lrt In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Built target tree_recon make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Building CXX object apps/yara/CMakeFiles/yara_indexer.dir/indexer.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/yara/CMakeFiles/yara_indexer.dir/indexer.cpp.o -MF CMakeFiles/yara_indexer.dir/indexer.cpp.o.d -o CMakeFiles/yara_indexer.dir/indexer.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:50: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/debug_test_system.h:150, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_debug.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:49, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:48: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/bits/stl_function.h:131:12: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/bits/stl_function.h:131:12: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/bits/stl_function.h:131:12: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:49: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | TSeqNameIt nameIt = begin(me.names[nameId], Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 201 | trimSeqNames(me.contigs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:209:34: required from ‘void trimSeqNames(SeqStore&) [with TSpec = void; TConfig = YaraContigsConfig<>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 209 | TSeqNameIt nameIt = begin(me.names[nameId], Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:201:21: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 201 | trimSeqNames(me.contigs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: recursively required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:195:14: required from ‘void loadContigs(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 195 | if (!open(me.contigsFile, toCString(me.options.contigsFile))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:357:16: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 357 | loadContigs(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, External > >; TString = String, Alloc<> >; TSpec = Owner > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, False) [with TSA = String >, External > >; TText = StringSet, Alloc<> >, Owner > > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 186 | _createSuffixArrayPipelining(sa, s, alg); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_aggregate.h:58, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:98: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:218:12: required from ‘void seqan::_createSuffixArrayPipelining(TSA&, const StringSet&, TAlgSpec) [with TSA = String >, External > >; TString = String, Alloc<> >; TSpec = Owner > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | struct Pipe< TInput, Multi > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:186:37: required from ‘void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, False) [with TSA = String >, External > >; TText = StringSet, Alloc<> >, Owner > > > >; TAlgSpec = Skew7]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 186 | _createSuffixArrayPipelining(sa, s, alg); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:198:34: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:56: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:243:12: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 243 | struct Pipe< TInput, Skew7 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 5, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:414:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 414 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 4, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:415:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 415 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:432:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 432 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:443:21: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 443 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: required from ‘seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 294 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TSpec = MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:416:33: required from ‘bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe, Alloc<> >, Source<> >, Caster, CasterReinterpret> >; TLimitsString = String >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool >, Tuple, Tuple, 4, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 4, BitPacked<> >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool >, Tuple, Tuple, 5, BitPacked<> >, Tag >, SorterSpec >, Tuple, Tuple, 5, BitPacked<> >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool >, Tuple, Tuple, 6, BitPacked<> >, Tag >, MapperSpec >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 416 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:350:34: required from ‘bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 350 | _skew7ExtendMulti( /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~^ 351 | textIn, limits, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~ 352 | names_S1, names_S2, names_S4, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 353 | sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:161:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 161 | if (r >= 6) push(out6, o6); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:162:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 162 | if (r >= 5) push(out5, o5); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:179:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 179 | if (r >= 3) push(out3, o3); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:190:17: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 190 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:633:42: required from ‘void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 633 | else handler2->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:904:28: required from ‘bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 904 | writer->end(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:786:13: required from ‘seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 786 | endWrite(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:173:12: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 173 | struct Pipe< TInput, Skew3 > /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 312 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple >, Tag >; TSpec = MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender7.h:163:29: required from ‘bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 3, int>, long unsigned int, File > > > >; TOut3 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut5 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 1, int>, long unsigned int, File > > > >; TOut6 = Pool, Tuple >, Tag >, SorterSpec, Tuple >, Tag >, 2, int>, long unsigned int, File > > > >; TOut124 = Pool, Tuple >, Tag >, MapperSpec, Tuple >, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 163 | if (r >= 4) push(out124, o4); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:362:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 362 | _skew7Extend(textIn, names_linear, sortedS0, sortedS3, sortedS5, sortedS6, sortedS124); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:312:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:123:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 123 | push(out0, o0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: required from ‘seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 218 | process(_textIn); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:376:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple >, Tuple, Tuple, 6, BitPacked<> >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended >, Tuple, Tuple, 6, BitPacked<> >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:447:21: required from ‘void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 447 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:465:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = short unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:337:28: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 337 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:622:44: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 622 | if (handler1) handler1->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:623:43: required from ‘void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 623 | else handler2->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:881:25: required from ‘void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 881 | writer->push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1167:16: required from ‘void seqan::push(Pool&, const TValue&) [with TValue = Triple, Tuple, Tag >; TSpec = MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 1167 | me.push(Val_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pump_extender3.h:101:17: required from ‘bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = Pipe >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >, Filter >, long unsigned int> > >; TNameInput = Pool >, MapperSpec >, long unsigned int>, long unsigned int, File > > > >; TOut0 = Pool, Tuple, Tag >, SorterSpec, Tuple, Tag >, int>, long unsigned int, File > > > >; TOut12 = Pool, Tuple, Tag >, MapperSpec, Tuple, Tag >, long unsigned int>, long unsigned int, File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 101 | push(out12, o2); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:269:29: required from ‘bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Filter >, long unsigned int> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 269 | _skew3Extend(textIn, names_linear, sortedS0, sortedS12); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:218:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple >, Tag >; TConfig = MapperConfigSize<_skew7NMapExtended, Tuple >, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:302:21: required from ‘void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, long unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, long unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, long unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 302 | ++in.in5; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:320:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple >, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h: In instantiation of ‘seqan::Buffer& seqan::processBuffer(Buffer >&, BufferHandler >, Tag >&) [with TValue = Triple, Tuple, Tag >; TConfig = MapperConfigSize<_skew3NMapExtended, Tuple, Tag >, long unsigned int>, long unsigned int, File > >; typename TConfig::File = File >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:332:33: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 332 | return processBuffer(*chain.first, *this); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:556:50: required from ‘seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >; TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 556 | else return handler2->next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_base.h:744:38: required from ‘void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 744 | buffer = handler.next(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24: required from ‘seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 870 | reader->pop(); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:111:17: required from ‘seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, long unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, long unsigned int>, long unsigned int, seqan::File > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 111 | ++in.in2; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:329:13: [ skipping 16 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_esa_stree.h:211:42: required from ‘seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > > > >, seqan::FMIndex > > >; TSpec = seqan::Preorder]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 211 | _indexRequireTopDownIteration(_index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:267:53: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 267 | typename Iterator >::Type it(index); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:303:55: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 303 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:316:42: required from ‘void saveIndex(YaraIndexer&) [with TContigsSize = unsigned char; TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 316 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:333:27: required from ‘void saveIndex(YaraIndexer&) [with TSpec = void; TConfig = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 333 | saveIndex(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/indexer.cpp:360:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: 360 | saveIndex(indexer); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: | ~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared ‘constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)’ is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/triple_packed.h:82:12: note: because ‘seqan::Triple, seqan::Tuple, seqan::Tag >’ has user-provided ‘seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]’ 82 | inline Triple(Triple const &_p) | ^~~~~~ [ 98%] Linking CXX executable ../../bin/yara_indexer cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_indexer.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_indexer.dir/indexer.cpp.o -o ../../bin/yara_indexer -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:280:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:290:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:424:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘insertStream’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:433:21: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘insertStream’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger3.h:127:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘operator++.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign.constprop.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘assign.constprop.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:129:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:328:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1665:1, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/priority_type_heap.h:289:11, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:260:31, inlined from ‘pop’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:613:42, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:870:24, inlined from ‘operator++’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_namer.h:114:13, inlined from ‘append’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1330:13, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1369:42, inlined from ‘assign’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1366:17, inlined from ‘operator<<’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_base.h:1376:22, inlined from ‘process.isra’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:345:26: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551536’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In member function ‘process.isra’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Built target yara_indexer make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Building CXX object apps/yara/CMakeFiles/yara_mapper.dir/mapper.cpp.o cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/g++ -DSEQAN_APP_VERSION=\"0.9.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/builddir/build/BUILD/seqan-seqan-v2.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/yara/CMakeFiles/yara_mapper.dir/mapper.cpp.o -MF CMakeFiles/yara_mapper.dir/mapper.cpp.o.d -o CMakeFiles/yara_mapper.dir/mapper.cpp.o -c /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:59, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:42, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:59: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 79 | struct FunctorUpcase : public std::unary_function | ^~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/random:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:51: /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 147 | struct FunctorConvert : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 219 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 228 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 237 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 246 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 255 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 264 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 276 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 287 | struct FunctorComplement : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:79: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 393 | struct PosLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file.h:92: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/file/string_external.h:1338:41: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 1338 | struct testIODone : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:45:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 45 | struct filterI1 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:54:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 54 | struct filterI2 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pipe_filter.h:63:35: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct filterI3 : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:74: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:351:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 351 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_mapper.h:457:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 457 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe.h:78: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:42:46: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 42 | struct MergeStreamComparer : public std::binary_function < PageBucket, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:57:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | public std::binary_function < | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:206:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 206 | struct insertBucket : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/pipe/pool_sorter.h:321:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 321 | struct insertBucket : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:48, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:46: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 325 | public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 63 | struct LessPairI1_ : public std::unary_function, bool> | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:47: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/misc/set.h:373:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 373 | struct SetLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:76: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:646:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 646 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:660:68: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 660 | struct FunctorGlobalize : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:666:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 666 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:714:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 714 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:782:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 782 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:851:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 851 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:885:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 885 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:933:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 933 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1814:33: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1814 | struct _qgramComp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_qgram.h:1833:13: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 1833 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:102: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:46:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 46 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_sa_qsort.h:85:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 85 | public std::binary_function < TSAValue, TSAValue, bool > | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:107: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:98:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 98 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:112:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 112 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:127:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 127 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:144:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew3.h:154:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:110: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:110:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 110 | public std::binary_function < SkewDCStream, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/pipe_merger7.h:143:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 143 | public std::binary_function < SkewDCStream >, Pack> >, | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:111: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:65:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 65 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:99:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 99 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:118:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 118 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:132:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 132 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:154:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 154 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:175:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 175 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7.h:185:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 185 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:114: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:57:43: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 57 | struct _skew7NCompMulti : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:97:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 97 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_skew7_multi.h:141:21: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 141 | public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:121: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:59:38: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 59 | struct _mapInverse : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_lcp.h:164:43: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 164 | struct _mapInverseMulti : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:125: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_bwt.h:144:44: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 144 | struct _filterGlobalizer : public std::unary_function { | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:131: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/index_shims.h:556:21: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 556 | public std::binary_function< Pair, Pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index.h:188: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/index/repeat_base.h:120:38: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 120 | struct RepeatLess_ : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:52, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/store_seqs.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:69: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fasta_fastq.h:221:39: warning: ‘template struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 221 | struct QualityExtractor : public std::unary_function | ^~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align.h:88, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io.h:50, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/bam_sam.h:39, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:224:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 224 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gap_anchor.h:234:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 234 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:60, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io/fai_index.h:41, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/seq_io.h:73: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:352:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 352 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:362:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 362 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:372:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 372 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:382:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 382 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:392:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 392 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_align.h:402:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 402 | public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/store/store_all.h:2155:17: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2155 | public std::binary_function< | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:91: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In function ‘void rankMatches(Mapper&, const TReadSeqs&)’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_function.h:1435: /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream.h:75, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/score.h:43, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:45: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /usr/include/c++/14/backward/binders.h:172:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /usr/include/c++/14/backward/binders.h:172:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /usr/include/c++/14/backward/binders.h:172:5: note: 739 | return _open(file, fileName, openMode, False()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 699 | if (!open(bamFile, bamFilename)) /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:98, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:75: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Sam_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:95: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const char*; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Bam_]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 159 | TLowcase lowcaseFileName(fileName); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:14: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 699 | if (!open(bamFile, bamFilename)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1326 | rankMatches(me, readSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 413 | configureMapper(options, threading, SingleEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1326 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1267:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1267 | rankMatches(me, readSeqs); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 425 | configureMapper(options, Serial()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:946:46: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 946 | removeIf(libraryLengths, std::bind2nd(std::greater(), 6.0 * libraryMedian), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:958:61: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = float]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 958 | transform(libraryDiffs, libraryLengths, std::bind2nd(std::minus(), libraryMean), typename TTraits::TThreading()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1328 | verifyMatches(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1405 | mapReads(me); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 1432 | runMapper(mapper); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /usr/include/c++/14/backward/binders.h:172:5: note: 415 | configureMapper(options, threading, PairedEnd()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /usr/include/c++/14/backward/binders.h:172:5: note: 422 | configureMapper(options, Parallel()); /usr/include/c++/14/backward/binders.h:172:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:97: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:140: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h: In instantiation of ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1269:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, All) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; All = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1269 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1405 | mapReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TContigsSum = long unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:425:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 425 | configureMapper(options, Serial()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 1109 | setHost(me.matesSetByCoord, me.matesByCoord); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: initializing argument 2 of ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ 294 | inline void setHost(StringSet > & me, typename Parameter_::Type host) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_smart_pointer.h:47, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_allocator.h:46, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:74, from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:57: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:205:36: required from ‘typename seqan::Parameter_::Type seqan::cargo(const ModifiedString >&) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 205 | return _toParameter(me._cargo); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:309:23: required from ‘bool seqan::empty(const ModifiedString >&) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 309 | return empty(cargo(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:858:18: required from ‘void rankMatches(Mapper&, const TReadSeqs&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 858 | if (empty(matches)) return TMatchesSize(0); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~^~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1326:16: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1326 | rankMatches(me, readSeqs); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:294:94: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 365 | return _object; | ^~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:96: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >, Alloc<> >; TSpec = SuffixSegment; typename Pointer_ >::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:296:30: required from ‘void seqan::setHost(StringSet >&, typename Parameter_::Type) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 296 | me.data_host = _toPointer(host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1109:12: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1109 | setHost(me.matesSetByCoord, me.matesByCoord); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: required from ‘void mapReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1237 | _mapReadsImpl(me, me.reads.seqs, typename TConfig::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1405:17: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFastq_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(PrefetchedFile >&, const char*) [with TFile = FormattedFile, Tag >; TRecords = SeqStore >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 151 | if (open(me.file, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:408:14: required from ‘void _openReadsImpl(Mapper&, SingleEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 408 | if (!open(me.readsFile, toCString(me.options.readsFile.i1))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:402:19: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_iterator.h:80, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:86: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TIterator = Iter, Alloc<> >, Owner > >, CountingIteratorImpl_ > >; TSpec = Tag; TIntegral = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 656 | TClassifier classifier(me.ctx, me.hits[0], me.seeds[0], me.options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1288:18: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 1288 | classifyReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::_toParameter(T&) [with T = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:279:31: required from ‘typename seqan::Parameter_::Type seqan::host(StringSet >&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; typename Parameter_::Type = Segment >, Alloc<> >, SuffixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 279 | return _toParameter(me.data_host); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/bits_bucket.h:182:17: required from ‘void seqan::bucket(StringSet >&, const TKeyGetter&, TMaxKey, const TThreading&) [with THost = Segment >, Alloc<> >, SuffixSegment>; TSpec = Segment >, Alloc<> >, SuffixSegment>; TKeyGetter = Getter >, const Tag >; TMaxKey = long unsigned int; TThreading = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 182 | forEach(host(me), TCounter(stringSetLimits(me), nextKey), tag); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1110:11: required from ‘void _verifyMatchesImpl(Mapper&, PairedEnd) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; PairedEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1110 | bucket(me.matesSetByCoord, Getter(), getReadsCount(me.reads.seqs), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1081:23: required from ‘void verifyMatches(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1081 | _verifyMatchesImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1328:22: required from ‘void _mapReadsImpl(Mapper&, TReadSeqs&, Strata) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, short unsigned int, unsigned int, long unsigned int, seqan::MMap<>, 3>; TReadSeqs = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 1328 | verifyMatches(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1237:18: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:351:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 351 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = short unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:381:34: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 381 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_type.h:358:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>&)’ is deprecated [-Wdeprecated-copy] 358 | return _object; | ^~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: because ‘seqan::Segment >, seqan::Alloc<> >, seqan::SuffixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >, seqan::Alloc<> >]’ 129 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = TagFasta_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: required from ‘bool seqan::open(PrefetchedFile >&, const char*) [with TFile = FormattedFile, Tag >; TRecords = SeqStore >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 151 | if (open(me.file, fileName)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:408:14: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_suffix.h:129:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence.h:94: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, Owner > >, PrefixSegment>; typename Iterator >::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, Owner > >, PrefixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, Owner > >, PrefixSegment>; typename Iterator >::Type = Iter, Alloc<> >, Owner > >, PrefixSegment>, AdaptorIterator, Alloc<> >, Owner > >, CountingIteratorImpl_ > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:24: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: required from ‘void classifyReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 656 | TClassifier classifier(me.ctx, me.hits[0], me.seeds[0], me.options); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1288:18: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/write_sam.h:114:14: required from ‘void seqan::write(TTarget&, const BamHeader&, const BamIOContext&, const Sam&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TNameStore = StringSet >, Owner > > >; TNameStoreCache = NameStoreCache >, Owner > > >, String > >; TStorageSpec = Dependent >; BamHeader = String; Sam = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | write(target, contigNames(context)[i]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:293:14: required from ‘void seqan::write(TTarget&, const BamHeader&, BamIOContext&, const TagSelector&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TNameStore = StringSet >, Owner > > >; TNameStoreCache = NameStoreCache >, Owner > > >, String > >; TStorageSpec = Dependent >; TTagList = TagList >; BamHeader = String]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 293 | write(target, header, context, TFormat()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_file.h:295:14: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Embl_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: required from ‘bool seqan::open(FormattedFile&, const char*, int) [with TFileFormat = Tag; TDirection = Tag; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 739 | return _open(file, fileName, openMode, False()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/file_prefetched.h:151:13: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const StringSet, Alloc<> >, Owner > >; TSpec = PrefixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, Owner > >, PrefixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: required from ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TIterator = Iter, Alloc<> >, Owner > >, CountingIteratorImpl_ > >; TSpec = Tag; TIntegral = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 577 | return Iter >(container(left), hostIterator(left) + right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:244:37: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = Segment, Alloc<> >, Owner > >, PrefixSegment>; TFunctor = ReadsClassifier, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Rooted_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 244 | TIter it = begin(c, iterTag) + splitter[i]; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:114:12: required from ‘void _classifyReadsImpl(ReadsClassifier&, Strata) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; Strata = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 114 | iterate(pairs, me, Rooted(), typename TConfig::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_classifier.h:76:27: required from ‘ReadsClassifier::ReadsClassifier(TReadsContext&, THits&, const TSeeds&, const Options&) [with TSpec = void; TConfig = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadsContext = ReadsContext, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THits = seqan::String >, seqan::Alloc<> >; TSeeds = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >, seqan::Segment, seqan::Alloc<> >, seqan::Owner > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 76 | _classifyReadsImpl(*this, typename TConfig::TStrategy()); //, typename TConfig::TAnchoring()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:656:17: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::Owner > >, seqan::PrefixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:216:27: required from ‘void seqan::setCargo(ModifiedString >&, typename Parameter_::Type) [with THost = String >, Alloc<> >; TPositions = Segment >, InfixSegment>; typename Parameter_::Type = Segment >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 216 | me._cargo = _toPointer(_cargo); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_position.h:357:13: required from ‘typename seqan::Infix > >::Type seqan::infix(ModifiedString >&, TPosBegin, TPosEnd) [with THost = String >, Alloc<> >; TPositions = String >; TPosBegin = long unsigned int; TPosEnd = long unsigned int; typename Infix > >::Type = ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 357 | setCargo(other, infix(cargo(me), pos_begin, pos_end)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:649:17: required from ‘typename seqan::Infix::Type seqan::infixWithLength(T&&, TPosBegin, TSize) [with T = ModifiedString >, Alloc<> >, ModPos > > >; TPosBegin = long unsigned int; TSize = long unsigned int; typename Infix::Type = ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 649 | return infix(t, pos_begin, pos_begin + length); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_set_segment.h:489:27: required from ‘typename seqan::InfixOnValue::Type seqan::value(const StringSet >&, TPos) [with THost = ModifiedString >, Alloc<> >, ModPos > > >; TSpec = ModifiedString >, Alloc<> >, ModPos > > >; TPos = long unsigned int; typename InfixOnValue::Type = const ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 489 | return infixWithLength(host(me), me.positions[pos], me.limits[pos + 1] - me.limits[pos]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_position.h:215:17: required from ‘typename seqan::Reference > > >::Type seqan::value(const Iter > >&) [with TContainer = const StringSet >, Alloc<> >, ModPos > > >, Segment >, Alloc<> >, ModPos > > >, InfixSegment> >; typename Reference > > >::Type = const ModifiedString >, Alloc<> >, ModPos >, InfixSegment> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 215 | return value(container(me), position(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:885:53: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = GenBank_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: required from ‘bool seqan::_open(FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = Tag; TDirection = Tag; TSpec = void; TThrowExceptions = False]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 722 | if (!guessFormatFromFilename(basename, file.format)) // read/write from/to a file (with extension) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:17: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1397 | openReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:90: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h: In instantiation of ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 455 | setQual(me.record, me.reads.seqs[readSeqId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _fillReadSeqQual(me, getReadSeqId(primary, me.reads.seqs)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 236 | _writeMappedRead(me, position(it, me.primaryMatches), primary, typename Traits::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:102:26: required from ‘void MatchesWriter::operator()(const TIterator&) [with TIterator = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 102 | _writeMatchesImpl(*this, it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const ModifiedString >, Alloc<> >, ModPos > > >, ModPos > > >; TFunctor = MatchesWriter, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:96:16: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:164:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 164 | TQualities qual(string); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:81: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h: In instantiation of ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const String >, Alloc<> >; TFunctor = HitsExtender, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 134 | iterate(me.hits, me, Standard(), typename Traits::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:220:25: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 220 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:62: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:221:27: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 221 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:241:21: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 241 | TNeedleInfixRev needleInfixRev(needleInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:242:23: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 242 | THaystackInfixRev haystackInfixRev(haystackInfix); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h: In instantiation of ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 429 | if (!_extendRight(extender, haystackRight, needleRight, matchEnd, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: required from ‘void seqan::iterate(TContainer&, TFunctor, const Tag&, Parallel) [with TContainer = const String >, Alloc<> >; TFunctor = HitsExtender, Tag, Tag, unsigned char, unsigned int, unsigned int, MMap<>, 3> > >; TIterTag = Standard_; Parallel = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 248 | f(it); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:134:12: required from ‘void _extendHitsImpl(HitsExtender&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 134 | iterate(me.hits, me, Standard(), typename Traits::TThreading()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:106:24: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:311:20: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 311 | THaystackInfix haystackPrefix(haystackInfix); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:312:18: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 312 | TNeedleInfix needlePrefix(needleInfix); | ^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:117:40: required from ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 117 | : data_container(_toPointer(container_)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: required from ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >; Rooted = const Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 351 | return TIterator(me, begin(me, Standard())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename RemoveReference::Type = Segment >, InfixSegment>; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/iter_stream.h:515:17: required from ‘typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const Segment >, InfixSegment>; TDirection = Tag; typename DisableIf >, typename Iterator >::Type>::Type = Iter >, InfixSegment>, AdaptorIterator > >; typename Iterator >::Type = Iter >, InfixSegment>, AdaptorIterator > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 515 | return begin(cont, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:1085:87: required from ‘typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = Iter, std::char_traits >, StreamIterator > >; TContainer = Segment >, InfixSegment>; typename EnableIf >, And >, Not::Type> > > > >, void>::Type = void; typename Value::Type = char]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1085 | typename DirectionIterator::Type iter = directionIterator(cont, Input()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/bam_io/write_sam.h:114:14: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h: In instantiation of ‘bool seqan::guessFormatFromFilename(const TFilename&, Tag) [with TFilename = Segment; TFormat_ = Raw_]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:36: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 114 | if (guessFormatFromFilename(fname, TFormat())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:120:35: required from ‘bool seqan::guessFormatFromFilename(const TFilename&, TagSelector&) [with TFilename = Segment; TTagList = TagList, TagList, TagList, TagList, TagList, TagList, TagList > > > > > > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 120 | return guessFormatFromFilename(fname, static_cast::Base &>(format)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:722:37: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:402:19: required from ‘void openReads(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | _openReadsImpl(me, typename TConfig::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1397:14: required from ‘void runMapper(Mapper&) [with TSpec = void; TConfig = ReadMapperConfig, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1397 | openReads(me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.h:1432:14: required from ‘void spawnMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TContigsSum = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1432 | runMapper(mapper); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared ‘constexpr seqan::Segment::Segment(const seqan::Segment&)’ is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: note: because ‘seqan::Segment’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]’ 117 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]’ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:151:25: required from ‘seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 151 | _host(_toPointer(host)), tmp_value() /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:164:16: required from ‘void setQual(seqan::BamAlignmentRecord&, const TString&) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 164 | TQualities qual(string); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:455:12: required from ‘void _fillReadSeqQual(MatchesWriter&, TReadSeqId) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadSeqId = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 455 | setQual(me.record, me.reads.seqs[readSeqId]); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:305:21: required from ‘void _writeMappedRead(MatchesWriter&, TReadId, const TMatch&, SingleEnd) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TReadId = long unsigned int; TMatch = Match >; SingleEnd = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 305 | _fillReadSeqQual(me, getReadSeqId(primary, me.reads.seqs)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:236:25: required from ‘void _writeMatchesImpl(MatchesWriter&, const TMatchIt&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; TMatchIt = seqan::Iter >, seqan::Alloc<> >, seqan::ModPos > > >, seqan::ModPos > > >, seqan::CountingIteratorImpl_ > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 236 | _writeMappedRead(me, position(it, me.primaryMatches), primary, typename Traits::TSequencing()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_writer.h:102:26: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:150:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = String, Alloc<> >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Alloc<> >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:220:25: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 220 | TNeedleInfixRev needleInfixRev(needleInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h: In instantiation of ‘typename seqan::Pointer_ >::Type seqan::_toPointer(Segment&) [with THost = const String, Packed > >; TSpec = InfixSegment; typename Pointer_ >::Type = Segment, Packed > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:118:25: required from ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 118 | _host(_toPointer(host)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:221:27: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 221 | THaystackInfixRev haystackInfixRev(haystackInfix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: required from ‘void HitsExtender::operator()(const THitsIterator&) [with THitsIterator = const Hit >*; TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | _extendHitImpl(*this, hitsIt, typename Traits::TStrategy()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/parallel/parallel_algorithms.h:248:14: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Packed > >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 243 | TFinderLeft finder(haystackInfixRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; typename RemoveReference::Type = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:317:18: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 317 | TFinderRight finder(haystackPrefix); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 429 | if (!_extendRight(extender, haystackRight, needleRight, matchEnd, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: required from ‘void _extendHitImpl(HitsExtender&, const THitsIterator&, const TStrategy&) [with TSpec = void; Traits = MapperTraits, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> >; THitsIterator = const Hit >*; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 216 | extend(me.extender, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~~ 217 | readSeq, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~ 218 | contigBegin, contigEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~ 219 | getValueI1(readPos), getValueI2(readPos), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 220 | hitErrors, maxErrors, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~ 221 | me); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:112:23: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:469:24: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(ModifiedString >&, Tag) [with THost = Segment, Packed > >, InfixSegment>; TTagSpec = Rooted_; typename Iterator >, const Tag >::Type = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 469 | TIterator temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:301:30: required from ‘seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 301 | : data_iterator(begin(haystack, Rooted())) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:243:17: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 243 | TFinderLeft finder(haystackInfixRev); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: required from ‘void extend(Extender&, const TNeedle&, THaystackPos, THaystackPos, TNeedlePos, TNeedlePos, TErrors, TMaxErrors, TDelegate&&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDistance = seqan::Tag; TSpec = void; THaystackPos = seqan::Pair >; TNeedlePos = long unsigned int; TErrors = long unsigned int; TMaxErrors = long unsigned int; TDelegate = HitsExtender, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | if (!_extendLeft(extender, haystackLeft, needleLeft, matchBegin, needleErrors, maxErrors)) return; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_extender.h:216:15: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/basic_fundamental.h:82, from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic.h:58: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Packed > >, InfixSegment>*; TParam = const Segment, Packed > >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Packed > >, InfixSegment>, Tag >; TValue = Segment, Packed > >, InfixSegment>; typename Value::Type = Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Packed > >, InfixSegment>; TValue2 = const Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Packed > >, InfixSegment>; TSource = Segment, Packed > >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h: In instantiation of ‘static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:305:28: required from ‘void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = Segment, Alloc<> >, InfixSegment>*; TParam = const Segment, Alloc<> >, InfixSegment>&]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 305 | TConstructor::construct(it, std::forward(param_)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:548:19: required from ‘typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = Holder, Alloc<> >, InfixSegment>, Tag >; TValue = Segment, Alloc<> >, InfixSegment>; typename Value::Type = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 548 | valueConstruct(ret, data); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:650:42: required from ‘void seqan::create(Holder >&, TValue2&) [with TValue = Segment, Alloc<> >, InfixSegment>; TValue2 = const Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 650 | me.data_value = _holderAllocateObject(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:887:15: required from ‘void seqan::assignValue(Holder >&, const TSource&) [with TValue = Segment, Alloc<> >, InfixSegment>; TSource = Segment, Alloc<> >, InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 887 | create(me, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/holder_tristate.h:135:20: required from ‘seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 135 | assignValue(*this, value_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/gaps_anchor.h:175:9: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:58: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:62: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:634:69: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 634 | TConstSeqHIterator seqHIterEndColumnTop = begin(seqH, Rooted()) + _min(seqHlength - 1, _max(0, upperDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Packed > >, InfixSegment>; TIterator = Iter, Packed > >, Packed > >; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:46: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: required from ‘TScoreValue seqan::globalAlignment(Gaps&, Gaps&, const Score&, const AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = Segment, Packed > >, InfixSegment>; TGapsSpecH = AnchorGaps > >; TSequenceV = Segment, Alloc<> >, InfixSegment>; TGapsSpecV = AnchorGaps > >; TScoreValue = int; TScoreSpec = Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = Tag; TAlgoTag = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 176 | TScoreValue res = _setUpAndRunAlignment(trace, dpScoutState, source(gapsH), source(gapsV), scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 | TAlignConfig2(lowerDiag, upperDiag), TGapModel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_aligner.h:146:27: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier.h:61: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h: In instantiation of ‘typename seqan::Container >::Type seqan::container(ModifiedIterator&) [with THost = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; TSpec = Tag; typename Container >::Type = ModifiedString, Packed > >, InfixSegment>, Tag >]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_interface.h:430:24: required from ‘void seqan::goEnd(TIterator&) [with TIterator = ModifiedIterator, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 430 | goEnd(it, container(it)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:737:10: required from ‘void seqan::goEnd(Finder&) [with THaystack = ModifiedString, Packed > >, InfixSegment>, Tag >; TSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 737 | goEnd(hostIterator(me)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1537:18: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1537 | goEnd(finder); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:246:16: required from ‘bool _extendLeft(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 246 | while (find(finder, needleInfixRev, extender.patternLeft, -static_cast(remainingErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:413:25: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 278 | TContainer cont(container(host(me))); | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of ‘seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find.h:55: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h: In instantiation of ‘typename seqan::Parameter_::Type seqan::container(Finder&) [with THaystack = Segment, Packed > >, InfixSegment>; TSpec = void; typename Parameter_::Type = Segment, Packed > >, InfixSegment>]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:989:66: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 989 | typename Size::Type const columns = length(container(finder)) + state.leftClip; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_ >&, int) [with TFinder = Finder, Packed > >, InfixSegment>, void>; TNeedle = Segment, Alloc<> >, InfixSegment>; TNeedle2 = Segment, Alloc<> >, InfixSegment>; TSpec = AlignTextBanded; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 1646 | return find(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:320:16: required from ‘bool _extendRight(Extender, TSpec>&, THaystackInfix&, TNeedleInfix&, THaystackPos&, TErrors&, TMaxErrors) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; THaystackInfix = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TNeedleInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TMaxErrors = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 320 | while (find(finder, needlePrefix, extender.patternRight, -static_cast(remainingErrors))) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:429:26: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_string.h:117:53: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_base.h:599:38: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 599 | return container(hostIterator(me)); | ^ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:993:52: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 993 | TConstSeqVIterator itV = begin(seqV, Rooted()) + _max(0, _min(seqVlength - 1, -lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 586 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator+(const Iter >&, TIntegral) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = const SimpleType*; TSpec = Tag; TIntegral = long int]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:994:55: required from ‘void seqan::_computeHammingDistance(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | TConstSeqVIterator itVEnd = begin(seqV, Rooted()) + _min(seqVlength - 1, lowerDiagonal(band) + seqHlength); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:612:32: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 612 | _computeHammingDistance(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoringScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 613 | dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 577 | return Iter >(container(left), hostIterator(left) + right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:624:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 624 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()) - _min(0, 1 + upperDiagonal(band)); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; typename RemoveReference::Type = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:631:45: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 631 | TConstSeqHIterator seqHIterBegin = begin(seqH, Rooted()) + _max(0, _min(seqHlength - 1, lowerDiagonal(band))); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Packed > >, InfixSegment>; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Packed > >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Packed > >, InfixSegment>, AdaptorIterator, Packed > >, Packed > >, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:650:29: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 650 | if (seqHIterBegin == end(seqH, Rooted()) - 1) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Packed > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed > >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Packed > >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed > >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed > >, seqan::Packed > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed > >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:381:19: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 381 | TSeqVIterator iter = seqBegin; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:891:38: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWiseBanded = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 891 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 892 | sequenceEntryForScore(scoringScheme, seqH, position(seqHIter)), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 893 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 894 | seqVBegin, seqVEnd, scoringScheme, cacheDiag, cacheVert, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 895 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:308:33: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&, const TGapModel&) [with TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; TGapModel = Tag; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 308 | return _setUpAndRunAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_iterator.h:72:7: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 72 | class ModifiedIterator /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:287:63: required from ‘void seqan::compare_(Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = const ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | typename Iterator::Type right_it = begin(right, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 323 | compare_(lexical, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 170 | compare(*this, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:750:38: required from ‘typename seqan::Size::Type seqan::lcpLength(const TLeft&, const TRight&) [with TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >; typename Size::Type = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 750 | typename Comparator::Type _lex(left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ^~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_extender.h:222:24: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:124:15: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 124 | : data_container(other_.data_container), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:392:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 392 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:509:41: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 509 | TConstSeqVIterator seqVBegin = begin(seqV, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 112 | int errors = _setUpAndRunAlignment(me.dpContext, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 113 | me.traceSegments, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 114 | me.dpScoutState, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ 115 | source(contigGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~ 116 | source(readGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~ 117 | Score(0, -1000, -999, -1001), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | TAlignConfig2()) / -999; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:520:23: required from ‘typename seqan::Iterator >::Type seqan::end(const T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 520 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:510:37: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 510 | TConstSeqVIterator seqVEnd = end(seqV, Rooted()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: required from ‘void verify(Verifier >&, const TNeedle&, THaystackPos, THaystackPos, TErrors, TErrors, TDelegate&) [with THaystack = seqan::StringSet, seqan::Packed > >, seqan::Owner > > >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THaystackPos = seqan::Pair >; TErrors = long unsigned int; TDelegate = AnchorsVerifier, seqan::Tag, seqan::Tag, unsigned char, unsigned int, unsigned int, seqan::MMap<>, 3> > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 112 | int errors = _setUpAndRunAlignment(me.dpContext, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 113 | me.traceSegments, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 114 | me.dpScoutState, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ 115 | source(contigGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~ 116 | source(readGaps), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~ 117 | Score(0, -1000, -999, -1001), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 118 | TAlignConfig2()) / -999; /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper_verifier.h:193:11: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 486 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:512:23: required from ‘typename seqan::Iterator >::Type seqan::end(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 512 | return _endDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:458:102: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 458 | typename Iterator< ModifiedString const, Tag const >::Type temp_(end(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:287:63: required from ‘void seqan::compare_(Lexical&, TLeft&, TRight&) [with TSpec = long unsigned int; TLeft = const ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = const ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | typename Iterator::Type right_it = begin(right, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:323:13: required from ‘void seqan::compare(Lexical&, const TLeft&, const TRight&) [with TSpec = long unsigned int; TLeft = ModifiedString, Packed > >, InfixSegment>, Tag >; TRight = ModifiedString, Alloc<> >, InfixSegment>, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 323 | compare_(lexical, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:170:16: required from ‘seqan::Lexical::Lexical(const TLeft&, const TRight&) [with TLeft = seqan::ModifiedString, seqan::Packed > >, seqan::InfixSegment>, seqan::Tag >; TRight = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = long unsigned int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 170 | compare(*this, left, right); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_lexical.h:750:38: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h: In instantiation of ‘typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; Rooted = const Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:385:25: required from ‘typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, Tag) [with T = Segment, Alloc<> >, InfixSegment>; TSpec = Rooted_; typename DisableIf::Type> >, typename Iterator >::Type>::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; typename RemoveReference::Type = Segment, Alloc<> >, InfixSegment>; typename Iterator >::Type = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 385 | return _beginDefault(me, tag_); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_reverse.h:503:103: required from ‘typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const ModifiedString >&, Tag) [with THost = Segment, Alloc<> >, InfixSegment>; TTagSpec = Standard_; typename Iterator >, const Tag >::Type = ModifiedIterator, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 503 | typename Iterator const, Tag const >::Type temp_(begin(host(me), Rooted())); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:994:21: required from ‘bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 994 | ndlEnd = end(needle, Standard()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1181:44: required from ‘bool seqan::_stateInit(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1181 | return _patternInitSmallStateBanded(finder, needle, state); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1535:24: required from ‘bool seqan::find(TFinder&, const TNeedle&, PatternState_, True, TFindBeginPatternSpec> >&) [with TFinder = Finder, Packed > >, InfixSegment>, Tag >, void>; TNeedle = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TNeedle2 = ModifiedString, Alloc<> >, InfixSegment>, Tag >; TSpec = FindPrefix; TFinderCSP = NMatchesNone_; TPatternCSP = NMatchesNone_; TFindBeginPatternSpec = void]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1535 | if (!_stateInit(finder, needle, state)) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/find/find_myers_ukkonen.h:1646:16: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:402:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 402 | return configureMapper(options, threading, sequencing, All()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:413:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 413 | configureMapper(options, threading, SingleEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h: In instantiation of ‘seqan::Iter > seqan::operator-(const Iter >&, int) [with TContainer = Segment, Alloc<> >, InfixSegment>; TIterator = SimpleType*; TSpec = Tag]’: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:382:27: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TDPCell = DPCell_ >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 382 | for (; iter != seqEnd - 1; ++iter) /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~^~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:453:18: required from ‘void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSeqHValue = SimpleType; TSeqVValue = SimpleType; TSeqVIterator = Iter, Alloc<> >, InfixSegment>, AdaptorIterator*, Tag > >; TScoringScheme = Score >; TColumnDescriptor = MetaColumnDescriptor, Tag >; TDPProfile = DPProfile_ >, Tag, TracebackOn, Tag > >, Tag >]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 453 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqHValue, seqVValue, seqBegin, seqEnd, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 454 | scoringScheme, cacheDiag, cacheVert, TColumnDescriptor{}, TDPProfile{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:515:18: required from ‘void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const DPProfile_&, const NavigateColumnWise&) [with TDPScout = DPScout_ >, If > >, Terminator_<>, Tag > >; TDPScoreMatrixNavigator = DPMatrixNavigator_ >, Tag, String >, Alloc<> > >, Tag, Tag >; TDPTraceMatrixNavigator = DPMatrixNavigator_, String >, DPTraceMatrix, Tag > > >, Tag >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoringScheme = Score >; TBand = DPBandConfig >; TAlignmentAlgo = GlobalAlignment_ >; TGapCosts = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; NavigateColumnWise = Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 515 | _computeTrack(scout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 516 | sequenceEntryForScore(scoringScheme, seqH, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 517 | sequenceEntryForScore(scoringScheme, seqV, 0), /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 518 | seqVBegin, seqVEnd, scoringScheme, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 519 | MetaColumnDescriptor(), dpProfile); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_algorithm_impl.h:1417:26: required from ‘typename seqan::Value::Type seqan::_computeAlignment(DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const DPBandConfig&, const DPProfile_&) [with TDPScoreValue = DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = String >, Alloc<> >; TTraceMatHost = String; TTraceTarget = String, Alloc<> >; TScoutState = DPScoutState_ >; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreScheme = Score >; TBandSwitch = Tag; TAlignmentAlgorithm = GlobalAlignment_ >; TGapScheme = Tag; TTraceFlag = TracebackOn, Tag > >; TExecPolicy = Tag; typename Value::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 1417 | _computeAlignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1418 | dpProfile, TNavigationSpec{}); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/align/dp_setup.h:287:29: required from ‘typename seqan::Value >::Type seqan::_setUpAndRunAlignment(DPContext, TTraceValue, TScoreMat, TTraceMat>&, String&, DPScoutState_&, const TSequenceH&, const TSequenceV&, const Score&, const AlignConfig2&) [with TScoreValue = int; TGapSpec = Tag; TTraceValue = unsigned char; TScoreMat = String >, Alloc<> >; TTraceMat = String; TTraceSegment = TraceSegment_; TSpec = Alloc<>; TDPScoutStateSpec = Tag; TSequenceH = Segment, Packed > >, InfixSegment>; TSequenceV = Segment, Alloc<> >, InfixSegment>; TScoreValue2 = int; TScoreSpec = Tag; TDPType = GlobalAlignment_<>; TBand = DPBandConfig >; TFreeEndGaps = FreeEndGaps_; TTraceConfig = TracebackOn, Tag > >; typename Value >::Type = int]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 287 | return _computeAlignment(dpContext, traceSegments, dpScoutState, seqH, seqV, scoringScheme, alignConfig._band, /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 288 | TDPProfile()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/find_verifier.h:112:39: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:347:57: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TContigsLen = unsigned int; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 347 | spawnMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:360:48: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TContigsSize = unsigned char; TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 360 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:377:33: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&, const TStrategy&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag; TStrategy = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 377 | configureMapper(options, threading, sequencing, strategy); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:399:31: required from ‘void configureMapper(const Options&, const TThreading&, const TSequencing&) [with TThreading = seqan::Tag; TSequencing = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 399 | return configureMapper(options, threading, sequencing, Strata()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:415:24: required from ‘void configureMapper(const Options&, const TThreading&) [with TThreading = seqan::Tag]’ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 415 | configureMapper(options, threading, PairedEnd()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/mapper.cpp:422:24: required from here /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: 422 | configureMapper(options, Parallel()); /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared ‘constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)’ is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/segment_infix.h:143:5: note: because ‘seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>’ has user-provided ‘seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]’ 143 | operator = (Segment const & source) | ^~~~~~~~ /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of ‘seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]’ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ [100%] Linking CXX executable ../../bin/yara_mapper cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara && /usr/bin/cmake -E cmake_link_script CMakeFiles/yara_mapper.dir/link.txt --verbose=1 /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -W -Wall -pedantic -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/yara_mapper.dir/mapper.cpp.o -o ../../bin/yara_mapper -lrt -lz -lbz2 In function ‘allocate’, inlined from ‘_allocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_alloc.h:372:13, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1532:28, inlined from ‘_reallocateStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1577:30, inlined from ‘_reserveStorage’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1679:83, inlined from ‘reserve’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1697:20, inlined from ‘resize_’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1725:45, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/string_base.h:1785:50, inlined from ‘resize’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1149:18, inlined from ‘eraseBack’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/sequence/sequence_interface.h:1259:11, inlined from ‘_toText’ at /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/arg_parse/arg_parse_ctd_support.h:88:30: /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/basic/allocator_interface.h:211:35: warning: argument 1 value ‘18446744073709551552’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 211 | data = (TValue *) operator new(count * sizeof(TValue)); | ^ /usr/include/c++/14/new: In function ‘_toText’: /usr/include/c++/14/new:131:26: note: in a call to allocation function ‘operator new’ declared here 131 | _GLIBCXX_NODISCARD void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [100%] Built target yara_mapper make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 0 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.NrrVgG + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 ++ dirname /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd seqan-seqan-v2.4.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 'INSTALL=/usr/bin/install -p' -C build/library make: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' make[1]: Nothing to be done for 'all'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/library/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/README.rst -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/CHANGELOG.rst -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/lib64/pkgconfig/seqan-2.pc -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/lib64/cmake/seqan2/seqan-config.cmake -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_cols.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_config.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_interface_wrapper.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_iterator_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_metafunctions.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/align_traceback.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/aligned_sequence_concept.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/alignment_algorithm_tags.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/alignment_operations.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_algorithm_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_align_simd_helper.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_band.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_cell.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_cell_affine.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_cell_dynamic.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_cell_linear.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_context.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_formula.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_formula_affine.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_formula_dynamic.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_formula_linear.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix_navigator.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix_navigator_score_matrix.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix_navigator_score_matrix_sparse.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix_navigator_trace_matrix.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_matrix_sparse.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_meta_info.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_profile.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_scout.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_scout_simd.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_setup.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_trace_segment.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_traceback_adaptor.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/dp_traceback_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/evaluate_alignment.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/fragment.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gap_anchor.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gapped_value_type.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_anchor.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_array.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_iterator_anchor.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_iterator_array.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/gaps_iterator_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_banded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_hirschberg_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_myers_hirschberg_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_myers_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_specialized.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/global_alignment_unbanded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_banded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_banded_waterman_eggert_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_enumeration.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_enumeration_banded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_enumeration_unbanded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_unbanded.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/local_alignment_waterman_eggert_impl.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/align/matrix_base.h -- Installing: 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/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/file_async.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/file_directory.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/file_forwards.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/file_sync.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/system_base.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/system_event_win.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/system/system_forwards.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/tabix_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/tabix_io/tabix_index_tbi.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/translation.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/translation/translation.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/translation/translation_tables.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/ucsc_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/ucsc_io/ucsc_file.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/ucsc_io/ucsc_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/ucsc_io/ucsc_record.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/read_vcf.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/vcf_file.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/vcf_header.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/vcf_header_record.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/vcf_io_context.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/vcf_record.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/vcf_io/write_vcf.h -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/include/seqan2/seqan/version.h make: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/library' + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 'INSTALL=/usr/bin/install -p' -C build/Release make: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles/seqan_library.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target seqan_library /usr/bin/make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/alf/CMakeFiles/alf.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target alf /usr/bin/make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/bs_tools/CMakeFiles/bisar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 1%] Built target bisar /usr/bin/make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/bs_tools/CMakeFiles/casbar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 3%] Built target casbar /usr/bin/make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/bs_tools/CMakeFiles/four2three.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target four2three /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/dfi/CMakeFiles/dfi.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 4%] Built target dfi /usr/bin/make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/compute_gain.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/compute_gain.dir/build.make apps/fiona/CMakeFiles/compute_gain.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/compute_gain.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 6%] Built target compute_gain /usr/bin/make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/fiona.dir/build.make apps/fiona/CMakeFiles/fiona.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/fiona.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 7%] Built target fiona /usr/bin/make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fiona/CMakeFiles/fiona_illumina.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fiona/CMakeFiles/fiona_illumina.dir/build.make apps/fiona/CMakeFiles/fiona_illumina.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fiona/CMakeFiles/fiona_illumina.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 9%] Built target fiona_illumina /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 10%] Built target fx_bam_coverage /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 12%] Built target fx_fastq_stats /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 14%] Built target gustaf /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 15%] Built target gustaf_mate_joining /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/insegt/CMakeFiles/insegt.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 17%] Built target insegt /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_sim.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 25%] Built target mason_sim /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_genome.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 26%] Built target mason_genome /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_methylation.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 28%] Built target mason_methylation /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 29%] Built target mason_frag_sequencing /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_variator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_variator /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_materializer.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 31%] Built target mason_materializer /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_simulator.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 32%] Built target mason_simulator /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_splicing.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 34%] Built target mason_splicing /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_tests.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 35%] Built target mason_tests /usr/bin/make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/micro_razers/CMakeFiles/micro_razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 37%] Built target micro_razers /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 39%] Built target roi_plot_thumbnails /usr/bin/make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/bam2roi.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 42%] Built target bam2roi /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 45%] Built target roi_feature_projection /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_global_1111 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_lcs /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 46%] Built target pair_align_local /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0000 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 48%] Built target pair_align_global_0001 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0010 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target pair_align_global_0011 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0100 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 51%] Built target pair_align_global_0101 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0110 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_0111 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 53%] Built target pair_align_global_1000 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1001 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 54%] Built target pair_align_global_1010 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1011 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 56%] Built target pair_align_global_1100 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1101 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 57%] Built target pair_align_global_1110 /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 59%] Built target pair_align_lib /usr/bin/make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/pair_align/CMakeFiles/pair_align.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 60%] Built target pair_align /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/param_chooser/CMakeFiles/param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 62%] Built target param_chooser /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 64%] Built target test_funcs_param_chooser /usr/bin/make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 65%] Built target rabema_prepare_sam /usr/bin/make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 67%] Built target rabema_build_gold_standard /usr/bin/make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_evaluate.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 68%] Built target rabema_evaluate /usr/bin/make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_do_search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 70%] Built target rabema_do_search /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers/CMakeFiles/razers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 71%] Built target razers /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 73%] Built target razers3 /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 75%] Built target razers3_simulate_reads /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_quality2prob.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 76%] Built target razers3_quality2prob /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/rep_sep/CMakeFiles/rep_sep.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 78%] Built target rep_sep /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sak/CMakeFiles/sak.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 79%] Built target sak /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sam2matrix/CMakeFiles/sam2matrix.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target sam2matrix /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/samcat/CMakeFiles/samcat.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 81%] Built target samcat /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_search.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 82%] Built target s4_search /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_join.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 84%] Built target s4_join /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 85%] Built target seqan_tcoffee /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/seqcons2/CMakeFiles/seqcons2.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 89%] Built target seqcons2 /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/sgip/CMakeFiles/sgip.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 90%] Built target sgip /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/snp_store/CMakeFiles/snp_store.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 92%] Built target snp_store /usr/bin/make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/splazers/CMakeFiles/splazers.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/splazers/CMakeFiles/splazers.dir/build.make apps/splazers/CMakeFiles/splazers.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/splazers/CMakeFiles/splazers.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 93%] Built target splazers /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/stellar/CMakeFiles/stellar.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 95%] Built target stellar /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/tree_recon/CMakeFiles/tree_recon.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 96%] Built target tree_recon /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_indexer.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/yara/CMakeFiles/yara_indexer.dir/build.make apps/yara/CMakeFiles/yara_indexer.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/yara/CMakeFiles/yara_indexer.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 98%] Built target yara_indexer /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/depend make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/yara/CMakeFiles/yara_mapper.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/make -f apps/yara/CMakeFiles/yara_mapper.dir/build.make apps/yara/CMakeFiles/yara_mapper.dir/build make[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[2]: Nothing to be done for 'apps/yara/CMakeFiles/yara_mapper.dir/build'. make[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [100%] Built target yara_mapper make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' make[1]: Nothing to be done for 'preinstall'. make[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/alf -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/alf/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/alf/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/alf/example/small.fasta -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/bisar -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/casbar -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/four2three -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/bs_tools/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/bs_tools/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/dfi -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/dfi/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/dfi/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/dfi/example/fasta1.fa -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/dfi/example/fasta2.fa -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/fiona -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/compute_gain -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/fiona/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/fiona/README -- Installing: 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'/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' Run Build Command(s): /usr/bin/cmake -E env VERBOSE=1 /usr/bin/gmake -f Makefile sak_doc gmake[1]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/gmake -f CMakeFiles/Makefile2 sak_doc gmake[2]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -S/builddir/build/BUILD/seqan-seqan-v2.4.0 -B/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 2 /usr/bin/gmake -f CMakeFiles/Makefile2 apps/sak/CMakeFiles/sak_doc.dir/all gmake[3]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles/seqan_library.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' gmake[4]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 0%] Built target seqan_library /usr/bin/gmake -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' gmake[4]: Nothing to be done for 'apps/sak/CMakeFiles/sak.dir/build'. gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Built target sak /usr/bin/gmake -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/depend gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/seqan-seqan-v2.4.0 /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak/CMakeFiles/sak_doc.dir/DependInfo.cmake "--color=" gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/gmake -f apps/sak/CMakeFiles/sak_doc.dir/build.make apps/sak/CMakeFiles/sak_doc.dir/build gmake[4]: Entering directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [ 50%] Generating README.sak.txt cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && ../../bin/sak --export-help=txt > README.sak.txt [100%] Generating sak.1 cd /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/apps/sak && ../../bin/sak --export-help=man > sak.1 gmake[4]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' [100%] Built target sak_doc gmake[3]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release/CMakeFiles 0 gmake[2]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' gmake[1]: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/sak -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sak/LICENSE -- Installing: 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/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/s4_search -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/s4_join -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/searchjoin/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/searchjoin/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/seqan_tcoffee -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/seqan_tcoffee/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/seqan_tcoffee/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/seqan_tcoffee/example/seq.fa -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/seqcons2 -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/seqcons2/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/seqcons2/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/sgip -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sgip/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sgip/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sgip/example/iso_m2D_m196.A01 -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sgip/example/iso_r01_m200.A00 -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/sgip/example/iso_r01_m200.A01 -- Installing: 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/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/stellar -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/stellar/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/stellar/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/stellar/example/NC_001474.fasta -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/stellar/example/NC_001477.fasta -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/stellar/example/reads.fasta -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/tree_recon -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/tree_recon/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/tree_recon/README -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/tree_recon/example/example.dist -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/yara_indexer -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/yara_mapper -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/yara/LICENSE -- Installing: /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/yara/README.rst make: Leaving directory '/builddir/build/BUILD/seqan-seqan-v2.4.0/build/Release' + chmod a+x /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/alf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/bam2roi /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/bed_sort.sh /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/bisar /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/casbar /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/compute_gain /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/dfi /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/fiona /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/four2three /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/fx_bam_coverage /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/gff_sort.sh /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/gustaf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/gustaf_mate_joining /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/insegt /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_frag_sequencing /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_genome /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_materializer /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_methylation /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_simulator /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_splicing /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/mason_variator /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/micro_razers /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/pair_align /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/param_chooser /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/rabema_build_gold_standard /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/rabema_evaluate /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/rabema_prepare_sam /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/razers /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/razers3 /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/rep_sep /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/roi_feature_projection /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/roi_plot_9.sh /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/roi_plot_thumbnails /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/roi_sort.sh /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/s4_join /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/s4_search /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/sak /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/sam2matrix /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/samcat /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/seqan_tcoffee /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/seqcons2 /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/sgip /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/snp_store /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/splazers /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/stellar /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/tree_recon /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/yara_indexer /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/yara_mapper + ln -s /usr/share/seqan2/pdf_plot_helper/plot.awk /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/plot.awk + ln -s /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/bin/ps2pswLinks.gawk + rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/libexec/seqan2/examples/ngs_roi/R + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/LICENSE + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/CHANGELOG.rst + rm -f /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2/README.rst + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 2.4.0-22.fc40 --unique-debug-suffix -2.4.0-22.fc40.aarch64 --unique-debug-src-base seqan2-2.4.0-22.fc40.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/seqan-seqan-v2.4.0 find-debuginfo: starting Extracting debug info from 44 files DWARF-compressing 44 files sepdebugcrcfix: Updated 44 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/seqan2-2.4.0-22.fc40.aarch64 23498 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/bin/roi_plot_9.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/roi_sort.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/gff_sort.sh from /bin/bash to #!/usr/bin/bash mangling shebang in /usr/bin/bed_sort.sh from /bin/bash to #!/usr/bin/bash + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: seqan2-apps-2.4.0-22.fc40.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.1rvsla + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + DOCDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-apps + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/README.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/CHANGELOG.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-apps + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.UvzxpS + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/alf/alf-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/bs_tools/bs_tools-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/dfi/dfi-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fiona/fiona-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/fx_tools/fx_tools-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/gustaf/gustaf-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/insegt/insegt-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/mason2/mason2-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/micro_razers/micro_razers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/ngs_roi/ngs_roi-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/pair_align/pair_align-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/param_chooser/param_chooser-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers/razers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/razers3/razers3-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rep_sep/rep_sep-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sak/sak-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sam2matrix/sam2matrix-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/samcat/samcat-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/searchjoin/searchjoin-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqan_tcoffee/seqan_tcoffee-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/seqcons2/seqcons2-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/sgip/sgip-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/snp_store/snp_store-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/splazers/splazers-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/stellar/stellar-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/tree_recon/tree_recon-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/yara/yara-LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/apps/rabema/rabema-COPYING /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-apps + RPM_EC=0 ++ jobs -p + exit 0 warning: absolute symlink: /usr/bin/plot.awk -> /usr/share/seqan2/pdf_plot_helper/plot.awk warning: absolute symlink: /usr/bin/ps2pswLinks.gawk -> /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk Provides: seqan = 0:2.4.0-22.fc40 seqan2-apps = 2.4.0-22.fc40 seqan2-apps(aarch-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/bash ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_4.2.0)(64bit) libgcc_s.so.1(GCC_4.5.0)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_2.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.17)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.19)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Obsoletes: seqan <= 0:1.4.2 Processing files: seqan2-headers-2.4.0-22.fc40.aarch64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4EKOWY + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + DOCDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-headers + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/README.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/CHANGELOG.rst /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/doc/seqan2-headers + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.eduPif + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-headers + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-headers + cp -pr /builddir/build/BUILD/seqan-seqan-v2.4.0/include/seqan/LICENSE /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64/usr/share/licenses/seqan2-headers + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(bzip2stream) bundled(zipstream) cmake(seqan) pkgconfig(seqan-2) = 2.4.0 seqan2-headers = 2.4.0-22.fc40 seqan2-headers(aarch-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/pkg-config cmake-filesystem(aarch-64) pkgconfig(zlib) Processing files: seqan2-examples-2.4.0-22.fc40.aarch64 Provides: seqan2-examples = 2.4.0-22.fc40 seqan2-examples(aarch-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan2-debugsource-2.4.0-22.fc40.aarch64 Provides: seqan2-debugsource = 2.4.0-22.fc40 seqan2-debugsource(aarch-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: seqan2-apps-debuginfo-2.4.0-22.fc40.aarch64 Provides: debuginfo(build-id) = 036126860e8a15749e1a2abb53842e63dd249095 debuginfo(build-id) = 0446783c4f99f64767cf894de4bc7a83a459aad2 debuginfo(build-id) = 0a8df858fdaf5cb3e313f635594308b2a55cf844 debuginfo(build-id) = 16746f97ec64dc85d06de9c04ede11ee5afc4bdf debuginfo(build-id) = 19158bb763c972c5e152309554e115eb12d86630 debuginfo(build-id) = 20d1dadbfb729760bd7cbe3d5417ba0f7385346a debuginfo(build-id) = 22d8eed4d9f9b54cc265746e9a066fa244de79d2 debuginfo(build-id) = 24c58744c6f1766d48cd457ed2f63102b8830746 debuginfo(build-id) = 28ebbdfd60f8b52647ba3deac1ba589d63f386c4 debuginfo(build-id) = 28fcc9855bbe5390413e7153962de5d38a2976e0 debuginfo(build-id) = 2940a706c0ca4f2adf0c6b20a09013eb034e51ba debuginfo(build-id) = 3baf04b74fe96829e07a32b59af62602cb6f136b debuginfo(build-id) = 3c23bce91ecfe96076c126fda4f277192dad8b10 debuginfo(build-id) = 431f39f3f93f6456a8853b416f9d6a26d0317a26 debuginfo(build-id) = 441abcb266eb8ef8070391751595ee4f569d7a65 debuginfo(build-id) = 49d40c633bbfd9c67f30f9050b92365363ff9fe3 debuginfo(build-id) = 509d648afa32af73994a70ce2b8ee29ba0d1e590 debuginfo(build-id) = 50d40fee791956423e73881c82d1ce71492f6cad debuginfo(build-id) = 574ccbf183fcaf6a3edfac59ef59feb8a4c9656c debuginfo(build-id) = 5b6f97d2df08be9c67350a6bb29e4153b7e157b9 debuginfo(build-id) = 5f0ef6e39d4644c336e4f97ffce62c6f3ec648c1 debuginfo(build-id) = 6bd35495ff22df2fd030252e93a536c6cf4b60c9 debuginfo(build-id) = 74da050e397826e5e8e47ba71150de45159ef375 debuginfo(build-id) = 783c2047fc6309ef3f936a2b7fc1983cf6f1195a debuginfo(build-id) = 7b92ad1de203b33cf5a8617851169ea3ebe21ec4 debuginfo(build-id) = 7d0b129dde757f170fa6f0ab2a0a72db75f2279f debuginfo(build-id) = 7f6b0cd57367167bf84cf95b65c137d5364b17a8 debuginfo(build-id) = 848c89fb3cf0723857cb9a34770a84d60b2b101d debuginfo(build-id) = 89a97f12659650878bc364f33c7e2f1a637fde47 debuginfo(build-id) = 93eed4375aec0b86b91ab5504afdfd6a1e08b1d0 debuginfo(build-id) = 9896541bd2944c72fb3008d06b2ef965106e2ddd debuginfo(build-id) = 9980edb71405940102d7e0f08d2925b6ee67f58c debuginfo(build-id) = 9a95f9f52178a08cb2c580512d1aa6cfb81e4bad debuginfo(build-id) = 9e39854c3725c406b77c9eadb210cb1a0ddd6b57 debuginfo(build-id) = a8db99741e6af8f46dfabef45350820e21470956 debuginfo(build-id) = aa3cff4fcf11f4e1e5be14782d0a0f260d3813a4 debuginfo(build-id) = ae70f04e5ffbf3f20848f244451b3c80a631da24 debuginfo(build-id) = ccb193dc8c6e985aae15daf48190339fbfd9e2a1 debuginfo(build-id) = d6777fd6abd6c8b02e3fc5b23a26c04d4fc561b8 debuginfo(build-id) = d8fb9f44bf884f5bc482e639dc3419da650b002e debuginfo(build-id) = db3a2fc8e242f0782e97549a4ac772b31f87ecce debuginfo(build-id) = ddcc31616e438a62a19dec2f064f4c32f061ebc7 debuginfo(build-id) = e1593ee4c5301e6dcf19a77d4edc30c2c0e1363d debuginfo(build-id) = eb3ffad124f5f29dd8f9786ae0b73e92a93f683f seqan2-apps-debuginfo = 2.4.0-22.fc40 seqan2-apps-debuginfo(aarch-64) = 2.4.0-22.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: seqan2-debugsource(aarch-64) = 2.4.0-22.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 Wrote: /builddir/build/RPMS/seqan2-debugsource-2.4.0-22.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/seqan2-headers-2.4.0-22.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/seqan2-examples-2.4.0-22.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/seqan2-apps-2.4.0-22.fc40.aarch64.rpm Wrote: /builddir/build/RPMS/seqan2-apps-debuginfo-2.4.0-22.fc40.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.w8fut3 + umask 022 + cd /builddir/build/BUILD + cd seqan-seqan-v2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/seqan2-2.4.0-22.fc40.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.AqrDDY + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/seqan-seqan-v2.4.0-SPECPARTS + rm -rf seqan-seqan-v2.4.0 seqan-seqan-v2.4.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: absolute symlink: /usr/bin/plot.awk -> /usr/share/seqan2/pdf_plot_helper/plot.awk absolute symlink: /usr/bin/ps2pswLinks.gawk -> /usr/share/seqan2/pdf_plot_helper/ps2pswLinks.gawk Finish: rpmbuild seqan2-2.4.0-22.fc40.src.rpm Finish: build phase for seqan2-2.4.0-22.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-aarch64-1706586999.654064/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/seqan2-2.4.0-22.fc40.src.rpm) Config(child) 58 minutes 49 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "seqan2-examples", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "aarch64" }, { "name": "seqan2-apps-debuginfo", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "aarch64" }, { "name": "seqan2", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "src" }, { "name": "seqan2-debugsource", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "aarch64" }, { "name": "seqan2-headers", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "aarch64" }, { "name": "seqan2-apps", "epoch": null, "version": "2.4.0", "release": "22.fc40", "arch": "aarch64" } ] } RPMResults finished